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Abstract
Dinoflagellates are known for their development of highly aberrant organelle genetic systems. Both their plastid and
mitochondrial genomes are extremely reduced in gene number and rearranged into numerous unconventional genomic
elements. Transcription processes are also elaborately modified including extensive RNA editing and trans-splicing. Some
The development of endosymbiotic organelles requires two replaced their peridinin plastid by a subsequent, or serial,
cells to learn to live together. Plastids and mitochondria owe endosymbiosis (Archibald 2009). The sources of these new
their existence to bacteria that became resident inside a host plastids have been diverse, including from haptophytes, dia-
eukaryote. The development of these organelles required toms, cryptomonads (all resulting in tertiary plastids), and
metabolic integration of the two cells, as well as molecular green algae (serial secondary plastids) (Archibald 2009).
harmonization of their genetic functions. Typically, the endo- Dinoflagellates, therefore, present multiple opportunities for
symbiont surrenders much of its genetic content to the host examining the process of host–endosymbiont cell
cell nucleus but still maintains a reduced genome expressed integration.
semiautonomously using retained bacterial expression ma- The best studied of these recent endosymbioses in
Letter
chinery (Gould et al. 2008; Barbrook et al. 2010). All mito- dinoflagellates is the gain of a haptophyte to create the
chondria are derived from a single ancient endosymbiotic tertiary plastid found in three dinoflagellate genera,
event, whereas plastids have migrated horizontally into new Karlodinium, Karenia, and Takayama. The origin of this
hosts through several subsequent endosymbioses. These plas- new endosymbiont is clear as it contains the distinctive
tid transfers occur when a eukaryote, already bearing a pri- haptophyte accessory pigments (190 -hexanoyloxy-
0
mary plastid, becomes an endosymbiont itself in a new host. fucoxanthin and 19 -butanoyloxy-fucoxanthin) in place of
Plastids derived this way are known as secondary plastids or peridinin and phylogenies using plastid genes strongly
tertiary plastids if the endosymbiont already bore a secondary group it with haptophytes (Tengs et al. 2000; Ishida and
plastid (Archibald 2009). With each new endosymbiosis, a Green 2002; Patron et al. 2006). This endosymbiont is now
new round of molecular harmonization must commence be- well integrated into its dinoflagellate host, with the endosym-
tween the host cell and symbiont. biont nucleus eliminated and only the photosynthetic plastid
Dinoflagellate algae are unusual among eukaryotes in that retained, surrounded by 3–4 membranes (Dodge 1989). Most
this phylum has gained plastid endosymbionts multiple dif- endosymbiont genes are relocated to the host nucleus and,
ferent times. The ancestor of dinoflagellates and their sister therefore, are under the direct control of the new host (Ishida
phylum, Apicomplexa, most likely inherited a common plas- and Green 2002; Takishita et al. 2004; Nosenko et al. 2006;
tid originally derived from a red algal endosymbiont Patron et al. 2006; Shalchian-Tabrizi et al. 2006; Gabrielsen
(Archibald 2009; Janouškovec et al. 2010). In photosynthetic et al. 2011). In Karlodinium veneficum, only 70 protein
dinoflagellates (approximately half have now lost photosyn- genes are retained in the plastid, encoded on the plastid
thesis), this ancestral plastid contains the distinctive pigment genome inherited from the haptophyte (Gabrielsen et al.
peridinin. Four dinoflagellate groups have more recently 2011).
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Mol. Biol. Evol. 30(4):788–792 doi:10.1093/molbev/mss270 Advance Access publication November 28, 2012 788
A Tertiary Plastid Gains RNA Editing in Its New Host . doi:10.1093/molbev/mss270 MBE
In this study, we present evidence that in K. veneficum, rpoB, and rpoC2 compared with E. huxleyi proteins affect
following endosymbiosis within the dinoflagellate host, plas- function in these cases). A second consequence of editing is
tid genetic processes have been re-engineered with the ac- a net increase in the A + T nucleotide content of plastid genes
quisition of an RNA editing system. From the recent 454 compared with transcripts, and this occurs predominantly at
assembly of the K. veneficum plastid genome, many gene codon position 1 then position 2 (table 2). The strong overall
sequences were noted as being unusual, including unex- A + T bias of this genome (72.9%, Gabrielsen et al. 2011) is
pected sequence divergence, the presence of canonical stop greatest at codon position 3 as this position least often con-
codons interrupting genes, and five genes with apparent strains the amino acid specified. Hence, the predominance of
frameshifts (Gabrielsen et al. 2011). To examine transcrip- A to G and U to C editing at positions 1 and 2 has allowed
tional processes in this endosymbiont, we generated gene further A + T drift to occur at these more limiting positions.
and transcript sequences corresponding to 14 plastid- Together these data indicate that RNA editing has allowed a
encoded genes (psaA, psbC, rbcL, atpG, atpI, rpl5, rps13, more extreme A + T rich genome to develop, while amelio-
rps18, rpl33, rpl36, petD, rpoB, rpoC2, and secY—totaling rating potential negative impacts to protein sequence and
7,373 nucleotides) including all five purported instances of function.
frameshifts, as well as cases of internal stop codons. We used a RNA editing in the K. veneficum plastid presents a dramatic
789
Jackson et al. . doi:10.1093/molbev/mss270 MBE
Table 1. RNA Editing Events in 14 Tertiary Plastid-Encoded Transcripts.
Gene Sequence RNA Edits Number gDNA Coding cDNA Coding Increase to
Identity to Identity to E. hux Protein
E. hux (%) E. hux (%) Identity After Editing (%)
A – G 26
a G – A 2
psaA (1,227 nt) C – U — 72.8 76.7 3.9
U – C 6
A – G 15
G – A 2
psbC (904 nt) C – U 1 79.0 82.0 3.0
U – C 7
A – G 4
G – A 1
rbcL (1,062 nt) C – U 2 83.3 83.6 0.3
U – C 4
A – G 7
Protein M
I F R I I Y
A L G V VH
100 198
rps13 RNA
Protein K N V Y R I I
E D A H K T T
199 297
rps13 RNA
Protein N K E Y Y*
D R GH HQ
298 351
rps13 RNA =A
=G
=U
Protein * =C
Table 2. Codon Positional A + T Content in 2,443 Plastid-Encoded editing system would have no immediate function. However,
Codons. once established, it might allow subsequent mutations to
Codon Position A + T% gDNA A + T% cDNA occur that are then reversed at the RNA level. In K. veneficum,
1st 56.5 53.0 one evolutionary consequence of adopting editing is an in-
2nd 64.1 61.8 crease in the A + T nucleotide bias of plastid genes compared
3rd 84.0 83.1 with the transcripts (and also compared with E. huxleyi where
All 68.2 66.0 the average A + T content of homologous sequences equals
61%). It is possible that there is some positive advantage for
allowing this increase in A + T content; however, such an
plastid have persisted in the host nucleus, and their proteins advantage is not obvious. If the K. veneficum plastid did use
are now targeted into the haptophyte tertiary plastid pre-existing editing machinery, then this would represent a
(Nosenko et al. 2006; Patron et al. 2006; Waller et al. 2006). good case of neutral evolution, cultivated by the novel genetic
Therefore, it is possible that either pre-existing plastid RNA environment of the dinoflagellate host. It is interesting to
editing machinery, or that for the existing mitochondrial note that the K. veneficum plastid genome has apparently
system (or even both), could have been recruited to this undergone further accelerated change after entering its dino-
new plastid and contributed to its development of editing. flagellate host, with substantial gene loss and genome re-
Confirmation of either hypothesis awaits knowledge of the arrangement, although not yet approaching the level of
RNA editing machinery in dinoflagellates. plDNA modification seen in peridinin plastids (Howe et al.
Why RNA editing has been recruited by this new dinofla- 2008; Gabrielsen et al. 2011). Although the mechanism caus-
gellate endosymbiont is a more challenging question and one ing these genomic changes is unclear, they provide further
that is equally relevant to RNA editing in all systems. It is evidence of the peculiar influence that the dinoflagellate en-
tempting to consider that editing evolved to correct muta- vironment can have on its new endosymbiotic partners.
tions after they occurred, and, indeed, editing appears to re- RNA editing in the related tertiary plastid of Karenia miki-
store K. veneficum plastid sequences to greater identity with motoi has been simultaneously reported (Dorrell and Howe
homologs (table 1), as is also the case in plant organelles 2012). Interestingly, both transition and transversion edits are
(Wakasugi et al. 2001). However, it is unlikely that evolution reported for K. mikimotoi, suggesting possible ongoing devel-
or recruitment of the necessary editosome complexity could opment of complexity of the plastid editing machinery in this
occur quickly enough to rescue spontaneous deleterious mu- lineage.
tations. Moreover, across eukaryotes, the presence of organ-
elle RNA editing systems negatively correlates with genome
Supplementary Material
mutation rates, suggesting that mutational pressure does not Supplementary data are available at Molecular Biology and
explain development of this form of genome complexity Evolution online (http://www.mbe.oxfordjournals.org/).
(Lynch et al. 2006). The theory of “constructive neutral evo-
lution” presents an alternative hypothesis, positing that de-
Acknowledgments
velopment of the machinery for editing precedes its This work was supported by an Australian Research Council
requirement (Lukes et al. 2011; Gray 2012). In such a scenario, Discovery grant (DP0663590) and by the University of
the gradual development or recruitment of a nondeleterious Melbourne Science Faculty Scholarship to C.J.J.
791
Jackson et al. . doi:10.1093/molbev/mss270 MBE
References and their integration into biological systems. New York: Wiley Press.
p. 280–309.
Archibald J. 2009. The puzzle of plastid evolution. Curr Biol. 19: Lukes J, Archibald JM, Keeling PJ, Doolittle WF, Gray MW. 2011. How a
R81–R88. neutral evolutionary ratchet can build cellular complexity. IUBMB
Barbrook AC, Howe CJ, Kurniawan DP, Tarr SJ. 2010. Organization and Life 63:528–537.
expression of organellar genomes. Phil Trans R Soc B. 365:785–797. Lynch M, Koskella B, Schaack S. 2006. Mutation pressure and the evo-
Chateigner-Boutin A-L, Small I. 2010. Plant RNA editing. RNA Biol. 7: lution of organelle genomic architecture. Science 311:1727–1730.
213–219. Nosenko T, Lidie KL, Van Dolah FM, Lindquist E, Cheng J-F, Bhattacharya
Dang Y, Green BR. 2009. Substitutional editing of Heterocapsa triquetra D. 2006. Chimeric plastid proteome in the Florida “red tide” dino-
chloroplast transcripts and a folding model for its divergent chloro- flagellate Karenia brevis. Mol Biol Evol. 23:2026–2038.
plast 16S rRNA. Gene 442:73–80. Patron NJ, Waller RF, Keeling PJ. 2006. A tertiary plastid uses genes from
Dodge JD. 1989. Phylogenetic relationships of dinoflagellates and their two endosymbionts. J Mol Biol. 357:1373–1382.
plastids. In: Green JC, Leadbeater BSC, Diver WL, editors. The chro- Salone V, Rüdinger M, Polsakiewicz M, Hoffmann B, Groth-Malonek M,
mophyte algae: problems and perspectives. Oxford: Clarenden Press.
Szurek B, Small I, Knoop V, Lurin C. 2007. A hypothesis on the
p. 207–227.
identification of the editing enzyme in plant organelles. FEBS Lett.
Dorrell G, Howe CJ. 2012. Functional remodeling of RNA processing in
581:4132–4138.
replacement chloroplasts by pathways retained from their prede-
Shalchian-Tabrizi K, Minge MA, Cavalier-Smith T, Nedreklepp JM,
cessors. Proc Natl Acad Sci U S A. 109:18879–18884.
Klaveness D, Jakobsen KS. 2006. Combined heat shock protein 90
792