Implications of mutation of organelle genomes for organelle function and evolution.

Journal of Experimental Botany Advance Access published June 15, 2015 Journal of Experimental Botany doi:10.1093/jxb/erv298

COMMENTARY

Implications of mutation of organelle genomes for organelle function and evolution John A. Raven* Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK † School of Plant Biology, University of Western Australia, M048, 35 Stirling Highway, Crawley, WA 6009, Australia

Received 28 January 2015; Revised 28 April 2015; Accepted 22 May 2015 Editor: Christine Raines

Abstract Organelle genomes undergo more variation, including that resulting from damage, than eukaryotic nuclear genomes, or bacterial genomes, under the same conditions. Recent advances in characterizing the changes to genomes of chloroplasts and mitochondria of Zea mays should, when applied more widely, help our understanding of how damage to organelle genomes relates to how organelle function is maintained through the life of individuals and in succeeding generations. Understanding of the degree of variation in the changes to organelle DNA and its repair among photosynthetic organisms might help to explain the variations in the rate of nucleotide substitution among organelle genomes. Further studies of organelle DNA variation, including that due to damage and its repair might also help us to understand why the extent of DNA turnover in the organelles is so much greater than that in their bacterial (cyanobacteria for chloroplasts, proteobacteria for mitochondria) relatives with similar rates of production of DNA-damaging reactive oxygen species. Finally, from the available data, even the longest-lived organelle-encoded proteins, and the RNAs needed for their synthesis, are unlikely to maintain organelle function for much more than a week after the complete loss of organelle DNA. Key words: Chloroplast, DNA damage, DNA repair, evolution, mitochondrion, mutation, phylogeny, protein turnover, reactive oxygen species.

Introduction After significant resistance from many biologists, the endosymbiotic origin of chloroplasts from cyanobacteria (Mereschowsky, 1905; Schmitz, 1982; Schimper, 1983; Martin and Kowallik, 1999), and then the endosymbiotic origin of mitochondria from (proteo)bacteria (Wallin, 1923), is now almost universally accepted (O’Malley, 2015). One, as yet, incompletely explained aspect of these energy-transducing organelles is the retention of an organelle genome in all chloroplasts and in all mitochondria, apart from some

hydrogenosomes. The organelle genome houses a small minority of the genes needed for organelle synthesis and function, the remainder having been transferred in evolution to the nucleus with translation on cytosol ribosomes and import of the resulting proteins into the organelle. The fraction of the organelle proteome encoded by the organelle genome has been estimated at 2.2% for Arabidopsis mitochondria (Heazlewood et al., 2004) and 3.5–5.3% for Arabidopsis chloroplasts (Abdellah et al., 2000; Kleffman et al., 2004). Allen

© The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: [email protected]

Downloaded from http://jxb.oxfordjournals.org/ at United Arab Emirates University on June 18, 2015

* To whom correspondence should be addressed. E-mail: [email protected] † Permanent address of JAR.

Page 2 of 12 | Raven significant experimental advances that help to bring into better focus some aspects of what remains to be discovered. Kumar et al. (2014) used two PCR-based techniques on chloroplast and mitochondrial genomes of developing Zea mays. The novel method is ‘molecular integrity PCR’ (miPCR) that quantifies long organelle DNA molecules that have no impediment to amplification and, hence, presumably, are functional in vivo in transcription and thence translation. The standard qPCR method gives the total number of copies, regardless of whether they could be functional in vivo in transcription and thus translation. They also measured ‘impediments’, including oxidative damage, using an in vitro DNA repair assay, as a check on impediments estimated from the qPCR methods. Part of the background to the work of Kumar et al. (2014) is the reported loss of all genomes from organelles during nonreproductive development in some organisms; there are two to many genomes per organelle early in cell development (Tables 1, 2). The first example to be reported is non-reproductive

Table 1. Copy number of mitochondrial and chloroplast genomes in Archeoplastida, i.e. with chloroplasts derived from a single primary endosymbiosis The general assumption is that the smallest unit detectable is the complete genome, or genome in process of replication, in the DAPI experiments of Kuroiwa et al. (1981). OrganismGlaucophyta Rhodophyta Cyanidiophyceae Rhodophyta Bangiophyceae Rhodophyta Florideophyceae Chlorophyta Prasinophyceae Chlorophyta Chlorophyceae Chlorophyta Trebouxiophyceae Chlorophyta Ulvophyceae Chlorophyta Charophyceae Streptophyta Embryophytes:Bryophyte (moss) Streptophyta Embryophytes: euphyllophyte: Pteridophyte Streptophyta Embryophytes; euphyllophyte: Glymnosperms Streptophyta Embryophytes: euphyllophyte Angiosperms

Mitochondrial genome copy number

24

Chloroplast genome copy number

References

1

Kuroiwa et al. (1981)

1–9 15–26

Kuroiwa et al. (1981) Hirakawa and Ishida (2014) Kuroiwa et al. (1981)

5–50


20–30


2–80

Kuroiwa et al. (1981) Hirakawa and Ishida (2014) Kuroiwa et al. (1981)

2–50 0–156

15–32

Kuroiwa et al. (1981) Lűttke (1988) Kuroiwa et al. (1981) Hirakawa and Ishida (2014) Kuroiwa et al. (1981)

6–23


8–16


0–900

Lamppa et al. (1980) Kuroiwa et al. (1981) Bendich and Gauriloff (1984) Bendich (1987) Kuroiwa et al. (1990) Rowan and Bendich (2009) Preuten et al. (2010) Wang et al. (2010)

10–300

0–2


and Raven (1996), Martin et al. (1998), and Race et al. (1999) discuss some of the reasons for the retention of genes in the organelle (e.g. the control of gene expression by the organelle redox status: Allen, 1993a, b; Allen and Raven, 1996; Allen, 2003; Allen et al., 2005) and for their relocation to the nucleus (e.g. the damage to DNA by the reactive oxygen species and other free radicals generated in the redox reactions of the organelles: Allen and Raven, 1996). Regardless of the reasons for the retention of genes in organelles, it is clear that changes in organelle DNA, including that resulting from oxidative damage, is greater than in the corresponding nuclear DNA, or bacterial or archaean DNA, under as nearly similar conditions as possible. However, much remains to be discovered about damage and other causes of changes to organelle DNA and its significance for short-term functioning of the organelles, their transmission to the next generation, and evolution. Many of the impediments to our understanding are technical, and Kumar et al. (2014) make

Organelle genomes for organelle function and evolution | Page 3 of 12 Table 2. Copy number of mitochondrial and chloroplast genomes in photosynthetic organisms with plastids from secondary or tertiary endosymbiosis Organism Discicristates Euglenophyta Rhizarians Chlorarachniophyta Chromalveolates Ochrophyta: Bacillariophyceae Chromalveolates Ochrophyta: Phaeophyceae Chromalveolates Ochrophyta: Raphidophyceae Chromalveolates Cryptophyta: Cryptophyceae

Mitochondrial genome copy number

18–40

24–43

Chloroplast genome copy number

References

20–34


30–50

Hirakawa and Ishida (2014)

1a


1a–16


10–40

Ersland et al. (1981)

22–260

Kuroiwa et al. (1981) Hirakawa and Ishida (2014)

While the general assumption is that the smallest unit detectable is the complete genome, or a genome in process of replication, in the DAPI experiments of Kuroiwa et al. (1981), there are clear exceptions. In many of the Ochrophyta the chloroplasts genome was recognized as a peripheral band within the chloroplast that was itself made up of the smallest detectable units (Kuroiwa et al., 1981).

development in the acellular green macroalga Acetabularia (Dasycladales; Ulvophyceae; Chlorophyta) (Woodcock and Bogorad, 1970; Coleman, 1979; Lüttke and Bonotto, 1981; Lüttke, 1988) using histochemical staining of DNA. Somewhat later, such a loss of chloroplast and mitochondrial genomes was reported, mainly using the more quantitative molecular genetic technique, in vegetative (somatic) cells in the developing leaves of flowering plants (Bendich and Gauriloff, 1984; Sodmergen et al., 1991; Rowan et al., 2002; Oldenburg and Bendich, 2004; Shaver et al., 2006; Preuten et al., 2010; Wang et al., 2010; Oldenburg et al., 2013), with changes in the integrity of the organelle DNA when it is retained (Oldenburg and Bendich, 2004; Shaver et al., 2006; Oldenburg et al., 2013). These conclusions on decreasing content, and even complete loss, of organelle DNA, and changes in organelle DNA integrity, during somatic cell development have been cogently challenged (Li et al., 2006; Zotschke et al., 2007). Possible means of reconciling the different conclusions resulting from variations in the developmental stage of the plant organ, and in experimental methods, have been suggested by Rowan and Bendich (2009) and outcomes of the relevant novel techniques mentioned in the Introduction (Kumar et al., 2014) are discussed in the following section. Pending complete resolution of these experimental differences, and the differences in the results obtained, one contribution of the present work is to explore the possibility of continued functioning of organelles after complete loss of their genomes.

Implications of advances in understanding organelle DNA integrity and copy number for understanding organelle genome function, inheritance, and evolution Organellar protein and DNA stability There has been much emphasis on oxidative and UV damage to DNA, and especially organelle DNA (Allen and Raven, 1996; Halliwell and Gutteridge, 2007) as part of causes of

variation in the DNA. The results of Kumar et al. (2014) are used as an example of the effects of of photosynthetically active radiation, with no specific UVB treatment, i.e. mainly reactive oxygen effects. Of the treatments they used, Kumar et al. (2014) found most damage, impediment, and in vitro repair for both chloroplasts and mitochondria in Zea mays plants grown in a 16/8 light/dark regime for 13 d, with less damage and impediment in plants in the dark for 12 d followed by 1 d in the light, and even less in plants in the dark for the full 13 d. The only difference between effects on chloroplasts and mitochondria occurs in light-grown plants. The qPCR-derived copy number on chloroplasts grown in the light is high, in agreement with measurements of damage, degree of impediment, fraction of unimpeded DNA from miPCR and in vitro repair, while in mitochondria the qPCR copy number is low in the light-grown plants, contrasting with the outcomes of the other methods. Oxidative and UV damage occurs to proteins as well as to DNA, and the relative roles of these of damage to the two macromolecules in causing cell death in environmentally challenged bacteria is, as discussed below, still a matter of debate (Daly et al., 2010). For the maintenance of organelle function over a significant fraction of the cell lifespan there is a need for the replacement of organelle- and nuclear-encoded proteins that have evaded the protective mechanisms (e.g. non-enzymic free radical scavengers, superoxide dismutase, ascorbate peroxidase) and have been damaged by oxidation and UV. This protein replacement requires the presence of organelle DNA and the RNAs and proteins associated with transcription and translation, or of long-lived mRNA and the RNAs and proteins associated with translation. Organelle-encoded proteins clearly do turn over, as shown for mitochondria of Saccharomyces cerevisae (de Jong et al., 2000; data on wild type) and chloroplasts of algae and plants (Table 3a). The half-lives for mitochondria-encoded proteins range from 185–415 h (Table 3a) and for chloroplast-encoded proteins range from 1.5–415 h (Table 3b). If the faster rates of breakdown also occurred in chloroplasts lacking DNA where, in the absence of


a

Page 4 of 12 | Raven Table 3a. Half-lives of mitochondrial genome-encoded RNAs and proteins Organism

t1/2 of RNA (h)

Arabidopsis thaliana

(11-fold range; no absolute values)

t1/2of protein (h)

References Giegé et al. (2000)

nad7 (complex I) 208 nad9 (complex I), 185 cox2 (complex IV), 185 atp8 (complex V) 238 ATP synthase (complex V), mean for mitochondrial- and nuclear-encoded subunits 415


Hordeum vulgare

Nelson et al. (2013)


Table 3b. Half-lives of chloroplast genome-encoded RNAs and proteins t1/2 of RNA (h)

Spinacia oleracea

psbA mRNA 5 (young), 10 (mature) rbcL mRNA 5 (young or mature) tRNA(lys) unspliced precursor 3 16S rRNA 20–40 psbA mRNA 40 atpH mRNA, 11–45 psbC mRNA, 11–19 psbA mRNA 33 rbcL mRNA 5.2–14

Hordeum vulgare


Chlamydomonas reinhardtii Brassica napus Chlamydomonas reinhardtii

Ostreococcus taurii

Hordeum vulgare

long-lived mRNA (see below), there could be no replacement of degraded protein, chloroplast function would be significantly decreased after a day and would be very limited after a few days. For mitochondria, there is also the maintenance of function after the loss of mitochondrial DNA. Using the qPCR method (Kumar et al., 2014), Preuten et al. (2010) showed that there were fewer copies of individual mitochondrial

t1/2 of protein(h)

Reference Klaff and Gruisson (1991)

Kim et al. (1993)

Germain et al. (2012)

psbA gene product (D1 protein), 1.5 psbA gene product (D1 protein) 2 petA gene product (cytochrome f) >21 petB gene product (cytochrome b6) >21 petD gene product (subunit IV of cytochrome b6-f complex) 20 ATP synthase components, 119–165 Core PSII proteins (not psbA), 136–204 rbcL, 147) Mean of chloroplastand nuclear-encoded subunits of: ATPsynthase, 116 Photosystem II (excluding psbA), 116 Photosystem I (excluding psaP) 415 psbA gene product (D1 protein), 17

Schuster et al. (1988) Sundberg et al. (1993) Gong et al. (2001); Mastrobuoni et al. (2012)

Martin et al. (2012


genes than of mitochondria in each mature cell. However, respiration rates are independent of mitochondrial gene number and, presumably, mitochondrial fission and fusion ‘share’ the genes among the mitochondria that can be counted at a particular time (Preuten et al., 2010). This is less likely for chloroplasts where fusion is very rare (CavalierSmith, 1970; Seguí-Simarro and Staehlin, 2009).


Organism

Organelle genomes for organelle function and evolution | Page 5 of 12 Table 3c. Half-lives of nuclear-encoded chloroplast proteins Organism

t1/2 of protein

Reference

Zea mays Arabidopsis thaliana Ostrecoccus tauri Nicotiana tabaccum

Rubisco (rbcL+rbcS), 168 h

Simpson et al. (1981); Piques et al. (2009) Martin et al. (2012) Krech et al. (2012)

Nicotiana tabaccum

Hordeum vulgare

Hojka et al. (2014)


Chloroplasts and mitochondria lacking DNA could retain synthesis of organelle-encoded proteins if the mRNAs for the proteins are long-lived and, of course, so would all of the post-translational components synthesis apparatus. Retention of the RNA and protein components needed for protein synthesis can be compromised by oxidative and UV damage, as is the case for organelle DNA and the organelleencoded proteins involved in functions other than protein synthesis. There seem to be no data on absolute rather than relative half-lives of mitochondria-encoded RNAs of plants or algae (Table 3a). The half-lives of chloroplast-encoded RNAs range from 3 h to 45 h (Table 3b). These values cannot be directly related, in the case of mRNAs, to the rate of decline in the synthesis of chloroplast-encoded proteins since this protein synthesis is translationally controlled (Fromm et al., 1985; Inamine et al., 1985; Hosler et al., 1989; Danon, 1997; Gilham et al., 1997; Eberhard et al., 2002, but see Udy et al., 2012), as is that of mitochondria-encoded proteins (Gilham et al., 1997; Holec et al., 2006). This means that an organelle mRNA might go through several decay half-lives before the amount of transcript becomes limiting for the rate of protein synthesis. Even with a several-fold increase in the effective (for protein synthesis) half-life of mRNA, if the faster rates of breakdown of mRNA and all of the posttranslational components synthesis apparatus also occurred in flowering plant chloroplasts lacking DNA, chloroplast function would be significantly decreased after several days and would be very limited after a week or two. The longest measured chloroplast mRNA half-life (Table 3b) would give a half-life of chloroplast proteins similar to the highest values for protein turnover (Table 3b). There seem to be no relevant data to determine if the damage to organelle-encoded proteins is more important than damage to the organelle genome for terminally differentiated organelles (i.e. not contributing to the next generation) in


rbcS 301 h Nuclear and plastid-encoded components of the PSI complex: ‘highly stable’ Nuclear and plastid-encoded components of the cytochrome b6-f complex: ‘lifetime at least one week’ Mean of chloroplast- and nuclear-encoded subunits of: ATPsynthase, 116 Photosystem II (excluding psbA), 116 Photosystem I (excluding psaA) 415 psbA gene product (D1 protein, chloroplast encoded), 17

multicellular organisms. Daly et al. (2010) have suggested, and provided evidence, that, even in the unicellular Deinococcus, damage to proteins is more significant than damage to DNA in determining survival under extreme conditions (see below). A parallel example of sustaining protein content in organelles despite damage to proteins and a lack of the encoding DNA is found for kleptoplastids. These are chloroplasts that have been retained within their cells by phagotrophs feeding on algae and remain photosynthetically functional for days or even months (Raven et al., 2009). In most cases, the nuclei of the food alga are not retained (e.g. in the relatively wellinvestigated sacoglossan marine gastropods), so that there is no possibility of replacing damaged nuclear-encoded chloroplast proteins unless there has been horizontal gene transfer from the algal nuclei to the phagotroph nucleus (Raven et al., 2009). While there have been claims of such horizontal gene transfer (Raven et al., 2009), the very thorough work of Wägele et al. (2011) showed that this was very unlikely, so the enigma of maintenance of the nuclear-encoded fraction of the chloroplast proteome of kleptoplastids remains. Even the capacity to express the chloroplast-encoded gene psbA (encoding the rapidly turning over D1 protein of photosystem II) requires a quality control gene (ftsH) that is nuclearencoded in streptophytes (Charophyta plus Embryophyta) (de Vries et al., 2013). However, the phylogenetic analysis of de Vries et al. (2013) shows that ftsH is chloroplast-encoded in the food algae Acetabularia acetabulum and Vaucheria litorea, providing the longest-functioning kleptoplastids (in the sacoglossans Elysia chlorotica and Elysia timida, respectively), so that quality control of D1 can be maintained. This important finding still does not explain how the many other nuclear-encoded gene products essential for photosynthesis, either directly as catalysts of photosynthetic reactions or as requirements for expression of chloroplast-encoded proteins (Zerges et al., 1997; Barkan and Goldschidt-Clermont, 2000) can be maintained in long-lived kleptoplastids. A further question arises from the use of Acetabularia chloroplasts as long-lived kleptoplastids, since, during vegetative growth, some Acetabularia chloroplasts apparently lack genomes (Lűttke, 1988). A further aspect of the dependence of kleptoplastids on the nuclear genome of the source alga concerns the fate of the glycolate resulting from Rubisco oxygenase and phosphoglycolate phosphatase in kleptoplastids. The production of glycolate cannot be suppressed by expression in the sacoglossan of inorganic carbon concentrating mechanisms (CCMs) from the host alga, since these CCMs typically have extraplastidial components encoded by algal nuclear genes (Falkowski and Raven, 2007; Raven et al., 2012, 2014), and so would not be acquired with the kleptoplastids. In the absence of a CCM (i.e. diffusive CO2 entry) glycolate is produced but cannot be metabolized since all but the initial and final steps of the photorespiratory carbon oxidation cycle are extraplastidial (Falkowski and Raven, 2007; Raven et al., 2012, 2014); the intermediate steps would not be acquired with the kleptoplastids. This has serious carbon balance and energetic consequences (Table 5.5 of Raven, 1984).

Page 6 of 12 | Raven

Is there a protected germline organelle genome in plants? The copy number of the mitochondrial and, in particular, the chloroplast genome has been measured with DNA dye and molecular genetic methods (Tables 1, 2). These techniques generally showed several or many copies of the plastid genome and (in algae) the mitochondrial genome, although no genomes could be detected in some plastids of an alga, and some mitochondria and chloroplasts of flowering plants (Tables 1, 2). The consequences of the absence of DNA from some organelles in vegetative growth are considered below. Reproduction and the means by which at least one organelle master genome, or its equivalent as subgenomic fragments, is inherited, is explored here (Bendich, 1987, 1993, 1996; Takanashi et al., 2010; Udy et al., 2012). Where there are multiple copies of the organelle genome in each organelle and/or many organelles per cell, then the probability is that each progeny cell at cell division will have at least one organelle genome (Bendich, 1987; Udy et al., 2012). This seems to be the case for chloroplasts (Tables 1, 2), although in some algae and the embryophytic hornworts and some cells of Selaginella there is only one chloroplast per cell and so they must rely on the first alternative, i.e. the presence of multiple genome copies in each organelle, in cell division. One or other (or both) alternative means of ensuring organelle genome

propagation also apply to algal mitochondria (Tables 1, 2). However, for flowering plant mitochondrial inheritance studies of egg cells of Arabidopsis, Wang et al. (2010) reported that 67% of egg cell mitochondria contained no DNA, and the 33% with DNA had an average of 109 kb DNA rather than the 366.9 kb for a mitochondrial master genome, i.e. the master genome is shared among mitochondria. This is also the case for Antirrhinium majus and Nicotiana tabacum, but not for Pelargonium zonale (Kuroiwa et al., 1990; Wang et al., 2010). The reported extent of the loss of functional organelle DNA during vegetative development in flowering plants correlates with the potential for plant regeneration from somatic cells (Shaver et al., 2006). Presumably the integrity of the master genomes (or their equivalent) could be because they have either been subject to fewer DNA changes, including that caused by damage, than occurs in leaf cells, or have had relatively complete repair so that their genomes are again in the master genome format; investigation is needed of the structural variation and recovery history of the organelle genomes between reproductive events. Embryophytes do not appear to have mechanisms similar to those in metazoans maintaining relatively structurally unchanged germ line mitochondria (Ivanov, 2007; de Paula et al., 2013). The ‘quiescent centre’ of flowering plant roots (Clowes, 1958; Dubrovsky and Barlow, 2015) has aspects of ‘stemness’, for example, a smaller electrical potential difference at the inner membrane of the mitochondria and low activities of tricarboxylic acid cycle enzymes (Jiang et al., 2006; de Paula et al., 2013), and retains organelle DNA turnover (Fujie et al., 1993). However, the cells in the root apex do not contribute to the production of the organs of sexual reproduction. For plant shoot apices, the selection of the least damaged mitochondria for incorporation into reproductive cells does not fit with the suggestion of Seguí-Simmaro and Staehlin (2009) of homogenization of mitochondrial DNA involving mitochondrial fusion and reticulation. Unicellular organisms have even less possibility of maintaining a germ line of organelles, especially if, as in the smallest known eukaryote, the picoplanktonic marine prasinophycean green alga Ostreococcus, there is only one chloroplast and one mitochondrion per cell (Blanc-Mathieu et al., 2013). This means that there are no organelles that are inactive in redox reaction and thus not as prone to oxidative damage as those that are active in redox reactions (de Paula et al., 2013). Although there seem to be no data on organelle genome copy number for Ostreococcus, other very small algal cells (e.g. the cyanidiophycean red alga Cyanidioschyzon merolae) have multiple copies of the genome in each organelle (Table 1; Hirakawa and Ishida, 2014). Is it possible that one (or more) of these copies represent a germ line while the rest do not? Also unicellular (or, better, acellular) is the large-celled green macroalga Acetabularia for which genome occurrence in chloroplasts has been investigated by dye staining (Woodcock and Bogorad, 1970; Coleman, 1979; Lüttke and Bonotto, 1981; Lüttke, 1988). This work on Acetabularia shows that young vegetative cells have genomes in all their chloroplasts;


Turning at last to measured half-lives of nucleus-encoded chloroplast proteins, Table 3c gives a range from 116–301 h for the most directly measured values, with the possibility of some even longer half-lives. However, there is also the possibility of nuclear-encoded proteins with shorter half-lives that would restrict the functional life of a kleptoplastid. While the t1/2 data in Table 3c do not readily explain the longest-lived kleptoplastids, it should be remembered that some mammalian erythrocytes function for months in an enucleate state. Gillooly et al. (2012) showed that, when the two determinants of erythrocyte life-span, i.e. temperature at which the erythrocytes function, and body mass of the animal in which they occur, are allowed for, there is no difference in life-span between enucleate mammalian erythrocytes and the erythrocytes of fish, amphibians, reptiles, and birds that are nucleate throughout their life, have functional mitochondria (Stier et al., 2013), and retain transcriptional activity (Moreira et al., 2011). While the habitat of a mammalian erythrocyte is significantly different from that of plastids, the erythrocyte data do show how long (over 104 h: Gillooly et al., 2012) enucleate cells can function despite the absence of protein synthesis. Raven (1991) pointed out that mature enucleate sieve tube elements would lack the capacity to replace damaged proteins and also suggested that low O2 concentrations in the sieve tube elements and the frequent occurrence of a lignified sheath round the vascular tissue would restrict damage from oxidative and UVB damage, respectively. However, the need for such protection is diminished by the demonstration of symplasmic protein movement from the nucleate companion cells to the enucleate sieve tube elements (Fisher et al., 1992; Oparka and Turgeon, 1999).

Organelle genomes for organelle function and evolution | Page 7 of 12

Structural variation is not correlated with the rate of evolution of organelle genomes An inevitable outcome of DNA damage and some other forms of structural variation (Kumar et al., 2014) is chemical alteration to nucleotides; without repair this would, at best, give rise to inherited nucleotide change in the genome and, at worst, the absence of replication or translation of the gene involved. In view of the technical and interpretation problems with the estimation of damage and other causes of variation to organelle DNA discussed by Kumar et al. (2014), it is difficult to obtain comparative data on the variation, either gross (without allowance for repair) or net (allowing for repair), among oxygenic photosynthetic organisms. There are, however, data on the rate of genetic change in one or more of the mitochondrial, chloroplastm and nuclear genomes. Early comparisons for flowering plants (Wolfe et al., 1987) showed that silent (synonymous) substitutions in mitochondrial DNA are less than one-third those of chloroplast DNA which, in turn, is half of that in nuclear DNA. The mean

silent substitution rate in plant mitochondrial DNA is one or two orders of magnitude less than that of metazoan mitochondrial DNA (Brown et al., 1979), while the rates for plant and metazoan nuclear DNA are similar (Wolfe et al., 1987). The rates of non-synonymous substitutions in plant mitochondria, chloroplasts, and nuclei are about an order of magnitude less than those of the corresponding synonymous substitutions (Wolfe et al., 1987: Table 4). Later work showed very high and variable mitochondrial substitution rates in Plantago spp. (Cho et al., 2004) and some other flowering plants (summarized by Smith et al., 2014a, b), and extremely low substitution rates in the mitochondrial DNA of Liriodendron and possibly even lower rates in the closely related Magnolia (Richardson et al., 2013). The synonymous substitution rate in the mitochondrial genome of flowering plants varies about 5000-fold (Richardson et al., 2013: Table 4). Of the plants examined by Richardson et al. (2013) Liriodendron and Magnolia had the lowest synonymous substitution rates in the chloroplast genome (though not as low as in mitochondria of these magnolids), with a 50-fold range in rates among flowering plants (Table 4). Despite the great variability in flowering plant mitochondrial genome synonymous substitution rates, with a much smaller range for plant chloroplast genomes, the general case for seed plants is for mitochondrial substitution rates to be less than the chloroplast rates, which are, in turn, less than the nuclear rates (Smith et al., 2014a, b), as concluded by Wolfe et al. (1987). Subsequent work on metazoans shows that the conclusion of Wolfe et al. (1987), which was based largely on vertebrates, as to the rate of synonymous substitution in mitochondrial genomes relative to the nuclear genome rate applies not just to the Deuterozoa (including vertebrates), but also the Ecdysozoa (e.g. arthropods), Lophotrochozoa (e.g. annelids and molluscs), platyhelminthes, and the medusozoan Cnidaria (Hellberg, 2006). Lower mitochondrial substitution rates are found in anthozoan Cnidaria and Porifera, resembling the rates in flowering plants and fungi (Hellberg, 2006). I hesitate to relate the similarity of substitution rates of Cnidaria, Porifera, flowering plants, and fungi to a shared sedentary habit. The situation with respect to the ranking of substitution rates among the three genomes is different in algae (Smith et al., 2014a, b: Table 4). Smith et al. (2014a, b) examined the synonymous substitution rates in the three genomes of Cyanophora paradoxa, a member of the basal (Glaucophyta) clade of the Archaeplastida (=Plantae sensu lato), and showed that the mitochondrial substitution rate was higher than both that in the chloroplasts and the similar rate in the nucleus. Smith et al. (2014a, b) review literature showing a similar pattern in another clade (Rhodophyta) of the Archaeplastida (Table 4). For the Haptophyta, an algal clade with secondarily endosymbiotic chloroplasts derived from the Rhodophyta, the mitochondrial rate is much higher than the chloroplast rate, although here the nuclear rate is rather higher than that of the chloroplast (Table 4; Smith et al., 2014a, b). For the other clade of the Archaeoplastida, the Chlorophyta (including an algal member of the Streptophyta), the rates of substitution for the three genomes are closely similar, i.e. still


as the alga continues vegetative growth an increasing fraction of the chloroplasts lack genomes, but that all chloroplasts in reproductive cells have genomes. There seem to be no data on the extent of oxidative or photochemical damage to DNA during vegetative growth, and during reproduction, in Acetabularia. Turning to variations in organelle function, there are significant genotypic differences in mitochondrial function among genotypes of Ostreococcus, as indicated by rhodamine as a measure of the proton motive force (proton electrochemical potential difference) across the inner mitochondrial membrane (Schaum and Collins, 2014), so any ‘germ line’ mechanism to maintain mitochondrial function as indicated by rhodamine does not work uniformly among genotypes. Some kind of germ line-like mechanism for vegetative cell division in diatoms may be involved in the results of Laney et al. (2012). Diatoms have overlapping frustules comprising the bipartite cell wall with larger (epitheca) and smaller (hypotheca) components. The new frustule components at vegetative cell division occur within the parental frustule components. The frustule forming inside the original epitheca forms a hypotheca that is the same size as the parental hypotheca, to produce a cell the same size as the parental cell. The parental hypotheca becomes the epitheca of the new cell, with a smaller new hypotheca formed inside it. Laney et al. (2012) showed that the ‘younger’ (smaller) cell had a greater specific growth rate than the ‘older’ (large) cell, to a greater extent than expected from the general specific growth rate–cell volume relationship of algae (see Fig. 3 of Finkel et al., 2010). Since the nuclei of the young and old cells should be essentially identical, could it be that the younger cells have inherited organelles that are less damaged at the nucleic acid and/or protein level? This possibility involves the sorting of more and less damaged organelles at cell division such as is known to occur in maintaining ‘stemness’ in mammalian stem cells (Katajisto et al., 2015).

Page 8 of 12 | Raven Table 4. Phylogenetic comparison of the rates of synonymous substitution in mitochondrial and chloroplast genomes relative to the rate in the corresponding nuclear genome Organism

Chloroplast genome substitution rate relative to nucleus=1

References

4.4

0.83

Smith et al. (2014a)

2.8

0.29

Smith et al. (2014a, b)

0.83 0.60

0.83 0.40

Smith et al. (2014a, b) Hirakawa & Ishida (2014)

0.25

0.5

Smith et al. (2014a, b)

0.06c

0.19d

Smith et al. (2014a,b)

Ersland et al. (1981) 2.8

0.29

Smith et al. (2014a, b) Hirakawa and Ishida (2014) Hirakawa and Ishida (2014)

a

Chlorophyta sensu stricto. Streptophyta sensu stricto. c 5000 fold range (Richardson et al., 2013) d 50 fold range (Richardson et al., 2013) b

different from the seed plants (embryophyte members of the Streptophyta) with the mitochondrial rate generally less than that of the chloroplast, and even less than that for the nucleus (summarized by Smith et al., 2014a, b: Table 4). Although it is unfortunate that there are no comparable rates of DNA damage for the organelle genomes for which nucleotide substitution rates are available, it seems unlikely that the substitution rates reflect differences in the rate of DNA damage.

Why are the rates of DNA turnover in organelles much higher than in their bacterial ancestors despite similar rates of production of oxidants? Despite the remaining technical problems (Kumar et al., 2014), there is an obvious contrast between the large potential extent of oxidative DNA damage in organelles and the bacterial ancestors of the organelles that have similar rates (perhaps slightly lower for bacteria) of redox reaction per unit volume to that of the organelles, and the much lower extent of DNA turnover in the bacteria. There are very limited data on the DNA turnover rates of organelles: organelle genomes of Euglena gracilis turn over, 1.5–1.6 times per generation, with minimal turnover of the nuclear genome (Manning and

Richards, 1972; Richards and Ryan, 1974). The minimal turnover of the Euglena nuclear genome is similar to that of the Proteobacteria (from which the mitochondrion was derived) and of the Cyanobacteria (from which the chloroplast was derived) (Bridges, 1997; Foster, 1999; Shirkey et al., 2003; Rajeev et al., 2013). The extant relatives of the organelle ancestors presumably have similar volume-based rates of oxidant production to those of the respective organelles: the rates may be lower in the free-living Cyanobacteria and Proteobacteria since they have to fulfil more non-bioenergetic cellular functions than is the case for the organelles. It may be more relevant to ask why organelle DNA is so prone to structural change, with substantial DNA turnover presumably based on the synthesis of unchanged DNA to replace changed DNA, rather than why their ancestors with similar exposure to conditions that damage DNA have much less DNA turnover. Even in extreme environmental conditions there is little oxidant damage to cyanobacterial DNA (Shirkey et al., 2003; Rajeev et al., 2013). Bendich (2007) point out that bacterial and archaeal genomes, like organelle genomes, do not generally consist entirely, or even largely, of ‘completed’ genomes, but contains a range of genomes sizes reflecting (among other things) different extents of replication of the complete genome. Furthermore, circular


Archaeoplastida Glaucophyta Cyanophora Archaeplastida Rhodophyta Porphyra Archaeplastida Chlorophyta s.l. Chlamydomonasa Mesostigmab Archaeplastida Seed plants Gymnosperms Archaeplastida Seed plants Angiosperms Ochrophyta Raphidophyceae Olisthodiscus Haptophyta Phaeocystis Cryptophyta Guillardia Chlorarachniophyta Bigelowia

Mitochondrial genome substitution rate relative to nucleus=1

Organelle genomes for organelle function and evolution | Page 9 of 12

Conclusions Organelle genomes are subject to variation, including that resulting from damage from reactive oxygen species, than are eukaryotic nuclear genomes or bacterial genomes under the same conditions. There have been, and still are, technical problems in characterizing this damage and other variation and its repair. Recent advances (Kumar et al., 2014) in the methodology for characterizing the variation of genomes of chloroplasts and mitochondria of Zea mays should, when applied more widely, help us to understand how variation in, including damage to, organelle genomes relates to maintenance of genome function during the life of individuals and of organelle genetic integrity in individuals and in succeeding generations. Understanding of the extent of variation in organelle DNA sequence and structure, and its repair, among photosynthetic organisms might also help to explain

the variations in the rate of inherited nucleotide substitution among organelle genomes, and its relation to inherited nucleotide substitution rate in nuclear genomes. Further studies of organelle DNA damage and repair might also help to understand why the extent of DNA turnover in the organelles is so much greater than that in their bacterial (cyanobacteria for chloroplasts, proteobacteria for mitochondria) relatives with similar rates of production of DNA-damaging reactive oxygen species. Finally, we would hope for a better understanding of the relation of organelle DNA damage to organelle protein damage and its repair; present data suggest that, after the loss of functional organelle DNA encoding a given protein, neither the lifetime of that protein nor of the RNA species needed to replace it using mRNA produced before DNA loss, can account for organelle function requiring that protein for much longer than a week.

Acknowledgements Discussions with John Allen, John Beardall, Jason Bragg, Sinéad Collins, Paul Falkowski, Zoe Finkel, Kevin Flynn, Mario Giordano, Stephen Hubbard, Andy Knoll, Hans Lambers, Tony Larkum, Antonietta Quigg, Patricia Sanchez-Baracaldo, and Elisa Schaum have been very helpful. Comments by two anonymous reviewers were very helpful in improving the manuscript.

References Abdellah F, Salamina F, Lesiter D. 2000. A prediction of the size and evolutionary origin of the proteome of Arabidopsis. Trends in Plant Science 5, 141–142. Allen JF. 1993a. Redox control of gene expression and function of chloroplast genomes: an hypothesis. Photosynthesis Research 36, 95–102. Allen JF. 1993b. Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genomes. Journal of Theoretical Biology 165, 609–631. Allen JF. 2003. The function of genomes in bioenergetics organelles. Philosophical Transactions of the Royal Society B 358, 19–38. Allen, JF, Puthiyaveetil S, Strőm J, Allen CF. 2005. Energy transduction anchors genes in organelles. Bioessays 27, 426–435. Allen JF, Raven JA. 1996. Free-radical-induced mutation vs. redox regulation: costs and benefits of genes in organelles. Journal of Molecular Evolution 42, 482–492. Barkan A, Goldschmidt-Clermont M. 2000. Participation of nuclear genes in chloroplast gene expression. Biochemie 82, 559–572. Bendich AJ. 1987. Why do chloroplasts and mitochondria contain so many copies of their genome? Bioessays 6, 279–282. Bendich AJ. 1993. Reaching for the ring: the study of mitochondrial genome structure. Current Genetics 24, 279–280. Bendich AJ. 1996, Structural analysis of mitochondrial DNA from fungi and plants using moving pictures and pulsed-field gel electrophoresis. Journal of Molecular Biology 255, 564–588. Bendich AJ. 2004. Circular chloroplast chromosomes: the grand illusion. The Plant Cell 16, 1661–1666. Bendich AJ. 2007. The size and form of chromosomes are constant in the nucleus, but highly variable in bacteria, mitochondria, and chloroplasts. Bioessays 29, 474–483. Bendich AJ, Gauriloff LP. 1984. Morphometric analysis of cucurbit mitochondria: the relationship between chondriome volume and DNA content. Protoplasma 119, 1–7. Bendich AJ, Smith SB. 1990. Moving pictures and pulse-field gel electrophoresis show linear DNA molecules from chloroplasts and mitochondria. Current Genetics 17, 421–425.


chromosomes are by no means universal among archaeal, bacterial, and organelle genomes (Bendich and Smith, 1990; Bendich, 2004, 2007; Shaver et al., 2008). The similarities in the occurrence of incomplete genomes in Archaea, Bacteria, and organelles clearly do not explain the differences in the rates of DNA turnover between organelle genomes and the genomes of Bacteria and Archaea. Deinococcus radiodurans is a bacterium with extreme resistance to treatments that damage DNA and proteins, i.e. ionizing (including gamma) radiation, desiccation, oxidation, and agents such as mitomycin C (Makarova et al., 2001; Daly et al., 2010; Slade and Radman, 2011). Deinococcus is closely related to Thermus, but otherwise is not closely related to other known Bacteria (Makarova et al., 2001). While it is not a close relative to the Proteobacteria from which mitochondria arose, Deinococcus is, like most interpretations of the functioning of the ancestral Proteobacteria giving rise to mitochondria, an aerobic chemo-organotroph. Mutant studies show that the characteristics of Deinococcus that permit resistance to extreme environments are not required for normal growth under non-extreme conditions (Makarova et al., 2001; Daly et al., 2010; Slade and Radman, 2011). Much of the emphasis on resistance to extreme conditions by Deinococcus has emphasized damage to DNA (Makarova et al., 2001), with such considerations as the minimum number (not more than five) of copies of the genome in each cell that are needed for resistance of extreme conditions. However, Daly et al. (2010) point out that the number of DNA doublestrand breaks caused by ionizing radiation in Deinococcus are similar to the number that occur in (for example) meiosis in eukaryotes without the need for special methods of DNA repair. Daly et al. (2010) emphasize the protection of protein from oxidative damage in Deinococcus, and have partially characterized a low molecular mass extract containing manganese, phosphate, and amino acids that acts to protect proteins from oxidative damage, for example, by removing hydroxyl radicals. However, this seems to have no direct relation to mechanisms protecting proteins from oxidative damage in mitochondria and chloroplasts.

Page 10 of 12 | Raven

Fujie M, Kuroiwa H, Suzuki T, Kawano S, Kuroiwa T. 1993. Organelle DNA synthesis in the quiescent centre of Arabidopsis thaliana (Col.). Journal of Experimental Botany 44, 689–693. Germain A, Kim SH, Gutierrez R, Stern DB. 2012. Ribonuclease II preserves chloroplast RNA homeostasis by increasing mRNA decay rates, and cooperates with polynucleotide phosphorylase in 3’ end maturation. The Plant Journal 72, 960–971. Giegé P, Hoffmann M, Binder S, Brennicke A. 2000. RNA degradation buffers assymetries of transcription in Arabidopsis mitochondria. EMBO Reports 1, 164–170.

Gilham NW, Boynton J, Rochaix JD. 1997. Translational regulation of gene expression in chloroplasts and mitochondria. Annual Review of Genetics 28, 71–93. Gillooly JF, Hayward A, Hou C, Burleigh JG. 2012. Explaining differences in the lifespan and replicative capacity of cells: a general model and comparative analysis of vertebrates. Proceedings of the Royal Society B 279, 3976–3980. Gong XS, Chung S, Fernández-Velasco JG. 2001. Electron transfer and stability of the cytochrome b6f complex in a small domain deletion mutant of cytochrome f. Journal of Biological Chemistry 276, 24365–24371. Halliwell B, Gutteridge JMC. 2007. Free radicals in biology and medicine , 4th edn. Oxford: Oxford University Press. Heazlewood JL, Tonti-Filippini JS, Gout AM, Day DA, Whelan J, Millar AH. 2004. Experimental analysis of the Arabidopsis mitochondrial proteome highlights signalling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins. The Plant Cell 16, 241–256. Hellberg ME. 2006. No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation. BMC Molecular Biology 6, 24. Hirakawa Y, Ishida K-Y. 2014. Polyploidy of endosymbiotically derived genomes in complex algae. Genome Biology and Evolution 6, 974–980. Hojka M, Theil W, Tóth SZ, Lein W, Bock R, Schöttler MA. 2014. Inducible repression of nuclear-encoded subunits of the cytochrome b6-f complex in tobacco reveals an extraordinarily long lifetime of the complex. Plant Physiology 165, 1632–1646. Holec S, Langer H, Kühn K, Alioua M, Börner T, Gagliardi D. 2006. Relaxed transcription in Arabidopsis mitochondria is counterbalanced by RNA stability control mediated by polyadenylation and polynucleotide phosphorylase. Molecular and Cellular Biology 26, 2869–2876. Hosler JP, Wurtz EA, Harris EH, Gillham NW, Boynton JE. 1989. Relationship between gene dosage and gene expression in the chloroplast of Chlamydomonas reinhardtii. Plant Physiology 91, 648–655. Inamine G, Nash B, Weissbach H, Brot N. 1985. Light regulation of the synthesis of the large subunit of ribulose-1.5-bisphosphate carboxylase in peas: evidence for translational control. Proceedings of the National Academy of Sciences, USA 82, 5690–5694. Ivanov VB. 2007. Stem cells in the root and the problem of stem cells in plants. Russian Journal of Developmental Biology 38, 338–349. Jiang K, Ballinger T, Li D, Zhang S, Feldman L. 2006. A role for mitochondria in the establishment and maintenance of the maize root quiescent center. Plant Physiology 140, 1118–1125. Katajisto P, Döhla J, Chaffer CL, Pentinmikko N, Marjanovic N, Iqbal S, Koncu R, Chen W, Weinberg RA, Sabatini DM. 2015. Asymmetric apportioning of aged mitochondria between daughter cells is required for stemness. Science 348, 340–343. Kim MY, Christopher DA, Mullet JA. 1993. Direct evidence for selective modulation of pdbA, rpoA, rbcL, and 16S-RNA stability during barley chloroplast debelopment. Plant Molecular Biology 22, 447–463. Klaff P, Gruisson W. 1991. Changes in chloroplast mRNA stability during leaf development. The Plant Cell 3, 517–529. Kleffman T, Rusenberger D, von Zychlinski A, Christopher W, Sjölander W, Bagicnky S. 2004. The Arabidiopsis thaliana chloroplast proteome reveals pathway abundance and reveal protein functions. Current Biology 14, 354–362. Krech K, Ruf S, Masduki FF, Thiele W, Bednarczyk D, Albus CA, Tiller N, Hasse C, Schöttler MA, Bock R. 2012. Thy plastid genomeencoded Ycf4 protein functioins as a non-essential assembly factor for photosystem I in higher plants. Plant Physiology 159, 579–591. Kumar RA, Oldenburg DJ, Bendich AJ. 2014.Changes in DNA damage, molecular integrity, and copy number for plastid DNA and mitochondrial DNA during maize development. Journal of Experimental Botany 65, 6425–6439. Kuroiwa T, Suzuki T, Ogawa K, Kawano S. 1981. The chloroplast nucleus: distribution, number, size, and shape, and a model for the multiplication of the chloroplast genome during chloroplast development. Plant and Cell Physiology 22, 381–396. Kuroiwa T, Kuroiwa H, Mita T, Fujie M. 1990. Fluorescence microscopy study of the formation of giant mitochondrial nuclei in the young ovules of Pelargonium zonale. Protoplasma 158, 191–194.


Blanc-Mathieu R, Sanchez-Ferandin S, Eyre-Walker A, Piganeau G. 2013. Organellar inheritance in the green lineage: insights from Ostreococcus tauri. Genome Biology and Evolution 5, 1503–1511. Bridges BA. 1997. DNA turnover and mutation in resting cells. Bioessays 19, 347–352. Brown WM, George Jr M, Wilson AC. 1979. Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences, USA 76, 1967–1971. Cavalier-Smith T. 1970. Electron microscopic evidence for chloroplast fusion in zygotes of Chlamydomonas reinhardii. Nature 228, 333–335. Cho Y, Mower JP, Qiu Y-L, Palmer JD. 2004. Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants. Proceedings of the National Academy of Sciences, USA 101, 17741–17746. Clowes FAL. 1958. Development of quiescent centres in roots meristems. New Phytologist 57, 85–88. Coleman AW. 1979. Use of the fluorochrome 4’6-diamido-2-phenylindole in genetic and developmental studies of chloroplast DNA. Journal of Cell Biology 82, 299–305. Daly MJ, Gaidamakova EK, Matrosova VY, Kiang JG, Fukumoto R, Leed DY, Wehr NB, Viteri GA, Berlett BS, Levine RL. 2010. Smallmolecule antioxidant protein shields in Deinococcus radiodurans. PLoS ONE 5, e12570. Danon A. 1997. Translational regulation in the chloroplast. Plant Physiology 115, 1293–1298. De Jong L, Elzinga SDJ, McCammon MT, Grivell LA, van der Spek H. 2000. Increased synthesis and decreaed stability of mitochondrial translatmion products in yeast as a result of loss of mitochondrial (NAD+)dependent isocitrate dehydrogenase. FEBS Letters 483, 62–66. De Paula WBM, Lucas CM, Agip A-NA, Vizcay-Barrena G, Allen JF. 2013. Energy, ageing, fidelity, and sex: oocyte mitochondrial DNA as a potential genetic template. Philosophical Transactions of the Royal Society of London B 368, 2012063. de Vries J, Habicht J, Woehle C, Huang C, Christa G, Wägele H, Nickelsen J, Martin WF, Gould SB. 2013. Is ftsH the key to plastid longevity in the sacoglossan slugs? Genome Biology and Evolution 5, 2540–2548. Dubrovsky JG, Barlow PW. 2015. The origins of the quiescent centre concept. New Phytologist 206, 493–496. Eberhard S, Finazzi G, Wollman F-A. 2002. Searching limiting steps in the expression of chloroplast-encoded proteins: relation between gene copy number, transcription, transcript abundance, and translation rate in the chloroplast of Chlamydomonas reinhardtii. The Plant Journal 31, 149–160. Ersland DR, Aldrich J, Cattolico RA. 1981. Kinetic complexity, homogeneity, and copy number of chloroplast DNAs for the marine alga Olisthodiscus luteus. Plant Physiology 68, 1468–1473. Falkowski PG, Raven JA. 2007. Aquatic photosynthesis ,2nd edn. Princeton; Princeton University Press. Finkel ZV, Beardall J, Flynn KJ, Quigg A, Rees TAV, Raven JA. 2010. Phytoplankton in a changing world: cell size and elemental stoichiometry. Journal of Plankton Research 32, 119–137. Fisher DB, Wu Y, Ku MSB. 1992. Turnover of soluble proteins in the wheat sieve tube. Plant Physiology 100, 1433–1441. Foster PL. 1999. Mechanisms of stationary phase mutation: a decade of adaptive mutation. Annual Review of Genetics 33, 57–88. Fromm H, Devic M, Fluhr R, Edelman M. 1985. Control of psbA gene expression: in mature Spirodela chloroplast light regulation of 32 kDa protein synthesis is independent of transcript level. EMBO Journal 4, 291–295.

Organelle genomes for organelle function and evolution | Page 11 of 12 Raven JA. 1991. Long-term functioning of enucleate sieve elements: possible mechanisms of damage avoidance and damage repair. Plant, Cell and Environment 14, 139–146. Raven JA, Beardall J, Giordano M. 2014. Energy costs of carbon dioxide concentrating mechanisms in aquatic organisms. Photosynthesis Research 121, 111–124. Raven JA, Beardall J, Flynn KJ, Maberly SC. 2009. Phagotrophy in the origins of photosynthesis in eukaryotes and as a complementary mode of nutrition in phototrophs: relation to Darwin’s insectivorous plants. Journal of Experimental Botany 60, 3975–3987. Raven JA, Giordano M, Beardall J, Maberly SC. 2012. Algal evolution in relation to atmospheric CO2: carboxylases, carbon-concentrating mechanisms and carbon oxidation cycles. Philosophical Transactions of the Royal Society B 367, 493–507. Richards OC, Ryan RS. 1974. Synthesis and turnover of Euglena gracilis mitochondrial DNA. Journal of Molecular Biology 82, 57–75. Richardson A, Rice DW, Alverson AJ, Young GJ, Palmer JD. 2013 The ‘fossilized’ mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutational rates. BMC Biology 11, 29. Rowan BA, Bendich AJ. 2009. The loss of DNA from chloroplasts as leaves mature; fact or artefact? Journal of Experimental Botany 60, 3005–3010. Rowan BA, Oldenburg DJ, Bendich AJ. 2002. The demise of chloroplast DNA in Arabidopsis. Current Genetics 46, 176–181. Schaum CE, Collins S. 2014. Plasticity predicts evolution in a marine alga. Proceedings of the Royal Society of London B 281, 201486. Schimper AFG. 1883. Ueber die Entwiselung der Chlorophyllkōrper und Farbkōrper. Flora oder Allgemeine Botanische Zeitung 41, 105–114, 121–131, 137–146, 153–162. Schmitz FAJ. 1882. Der Chromatophoren der Algen. Vergleichende Untersuchungen über Bau and Entwicklung der Chlorophyllkōrper und der analogen Farbstoffkōrper der Algen. Bonn Verlag von Max Coghen & Sohn (Dr. Cohen). Schuster G, Timberg R, Ohad I. 1988. Turnover of thylakoid photosystem II proteins during photoinhibition of Chlamydomonas reinhardtii. European Journal of Biochemistry 177, 403–410. Seguí-Simarro JM, Staehlin LA. 2009. Mitochondrial reticulation in shoot apical meristem cells of Arabidopsis provides a mechanism of homogenisation of mtDNA prior to gamete formation. Plant Signalling and Behaviour 4, 168–171. Shaver JM, Oldenburg DJ, Bendich AJ. 2006. Changes in chloroplast DNA during development in tobacco, Medicago, pea, and maize. Planta 224, 72–82. Shaver AM, Oldenberg, DJ, Bendich AJ. 2008. The structure of chloroplast DNA molecules and the effect of light in the amount of chloroplast DNA during development of Medicago trunculata. Plant Physiology 146, 1064–1074. Shirkey B, McMaster NJ, Smith SC, Wright DJ, Rodriguez H, Jaruga P, Birincioglu M, Helm RF, Potts M. 2003. Genomic DNA of Nostoc commune (Cyanobacteria) becomes covalently modified during longterm (decades) desiccation but is protected from oxidative damage and degradation. Nucleic Acids Research 31, 2995–300. Simpson E, Cooke RJ, Davies DD. 1981. Measurement of protein degradation in leaves of Zea mays using [3H] acetic anhydride and tritiated water. Plant Physiology 67, 1214–1219. Slade D, Radman M. 2011. Oxidative stress resistance in Deinococcus radiodurans. Microbial and Molecular Biology Reviews 75, 133–191. Smith DR, Jackson CJ, Reyes-Prieto A. 2014a. Nucleotide substitution rate of the glaucophyte Cyanophora suggest an ancestrally lower mutation rate in plastid vs mitochondrial DNA for the Archaeplastida. Molecular Phylogenetics and Evolution 79, 80–184. Smith DR, Arrigo KR, Aldekamp A-C, Allen AE. 2014b. Massive differences in synonymous substitution among mitochondrial, plastid, and nuclear genes of Phaeocystis algae. Molecular Phylogenetics and Evolution 71, 36–40. Sodmergen, Kawano S, Tabo S, Kuroiwa T. 1991. Degradation of chloroplast DNA in the second leaves of rice (Oryza sativa) before leaf yellowing. Protoplasma 160, 89–98.


Lamppa GK, Elliot LV, Bendich AJ. 1980. Changes in chloroplast number during pea leaf development. Planta 148, 437–443. Laney SR, Olsen RJ, Sosik HM. 2012. Diatoms favour their younger daughters. Limnology and Oceanography 57, 1572–1578. Li W, Ruf S, Bock R. 2006. Constancy of organellar genome copy numbers during leaf development in higher plants. Molecular Genetics and Genomics 275, 185–192. Lűttke A. 1988. The lack of chloroplast DNA in Acetabularia mediterranea (acetabulum) (Chlorophyceae): a reinvestigation. Journal of Phycology 24, 173–180. Lűttke A, Bonotto S. 1981. Chloroplast DNA of Acetabularia mediterranea: cell cycle related changes in distribution. Planta 153, 536–542. Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, Koonin EV, Daly MJ. 2001. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbial Molecular Biology Reviews 65, 44–79. Manning JE, Richards OC. 1972. Synthesis and turnover of Euglena gracilis nuclear and chloroplast deoxynucleic acid. Biochemistry 11, 2036–2043. Martin S, Mungapati VS, Salvo-chirnside E, Kerr LE, Le Bihan T. 2012. Proteome turnover in the green alga Ostreococcus tauri by timecourse, 15N metabolic labelling mass spectrometry. Journal of Proteome Research 11, 476–486. Martin W, Kowallik KV. 1999. Annotated English translation of Mereschowsky’s, 1905 paper ‘Uber Natur und Ursprung der Chromatophoren in Pflanzenreiche’. European Journal of Phycology 34, 287–295. Martin W, Stoebe B, Gorymekin V, Henesmann S, Hasegawa M, Kowallik KV. 1998. Gene transfer to the nucleus and the evolution of chloroplasts. Nature 393, 162–165. Mastrobuoni G, Igang S, Pietzke M, Wenzel M, Assmus HE, Schulze WX, Kempa S. 2012. Proteome dynamics and early salt stress response of the photosynthetic organism Chlamydomonas reinhardtii. BMC Genomics 13, 215. Mereschowsky C. 1905. Uber Natur und Ursprung der Chromatophoren in Pflanzenreiche. Biologische Centralblatte 25, 583–694. [English translation by Martin and Kowallik, 1999.] Moreira D, Roher N, Ribas L, et al. 2011. RNA-Seq reveals integrated immune response in nucleated erythrocytes. PLoS ONE 6, e26998. Nelson CJ, Alexova R, Jacoby RP, Millar AH. 2014. Proteins with high turnover rate in barley leaves estimated by proteome analysis combined with in planta isotope labelling. Plant Physiology 166, 91–108. Nelson CJ, Li L, Jacoby RP, Miller AH. 2013. Degradation rates of mitochondrial proteins in Arabidopsis thaliana cells. Journal of Proteome Research 12, 3449–3459. Oldenburg DJ, Bendich AJ. 2004. Changes in the structure of DNA molecules and the amount of DNA per plastid during chloroplast development in maize. Journal of Molecular Biology 344, 1311–1330. Oldenburg DJ, Kumar RA, Bendich AJ. 2013. The amount and integrity of mtDNA in maize with development. Planta 237, 603–617. O’Malley MA. 2015. Endosymbiosis and its implications for evolutionary theory. Proceedings of the National Academy of Sciences, USA (in press) doi:, 10.1073/pnas.1421389112. Oparka K, Turgeon R. 1999. Sieve elements and companion cells: traffic control centers of the phloem. The Plant Cell 11, 739–750. Piques M, Schulze WX, Höhne M, Usadel B, Gibon Y, Rohwer J, Stitt M. 2009. Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Molecular Systems Biology 5, 314. Preuten T, Cineu E, Fuchs J, Zoschke R, Liere K, Börner T. 2010. Fewer genes than organelles: extremely low and variable gene copy numbers in mitochondria of somatic plant cells. The Plant Journal 64, 948–959. Race HL, Herrmann RE, Martin W. 1999. Why have organelles retained genomes? Trends in Genetics 16, 164–370. Rajeev L, Nunes da Rocha U, Klitgord N, et al. 2013. Dynamic cyanobacterial in a desert biological soil crust. The ISME Journal 7, 2178–2191. Raven JA. 1984. Energetics and transport in aquatic plants . New York: AR Liss.

Page 12 of 12 | Raven Stier A, Bize P, Schull Q, Zall J, Singh F, Geny R, Gros F, Royer C, Messeminn S, Criscuolo F. 2013. Avian erythrocytes have functional mitochondria, opening novel perspectives for birds as animal models in the study of aging. Frontiers in Zoology 10, 33. Sundberg C, McCaffery S, Anderson JM. 1993. Turnover of Photosystem II D1 protein in higher plants under photoinhibitory and nonphotoinhibitory irradiance. Journal of Biological Chemistry 268, 25476–25482. Takanashi H. Ohnishi T, Mogi M, Okamoto T, Arimura S-I, Tsutsumi N. 2010. Studies of mitochondrial morphology and DNA content in the rice egg cell. Current Genetics 56, 33–41. Udy DB. Belcher S, Williams-Carrier R, Gualberto JM, Barkan A. 2012. Effects of reduced chloroplast gene copy number on chloroplast gene expression in maize. Plant Physiology 160, 1420–1431. Wägele H, Deusch O, Händeler K, et al. 2011. Transcriptomic evidence that longevity of acquired plastids in the photosynthetic slugs Elysia timida and Plakobranchus ocellatus does not entail lateral gene transfer of algal nuclear genes. Molecular Biology and Evolution 28, 699–706.

Wallin JE. 1923. The mitochondria problem. American Naturalist 57, 255–261. Wang D-Y, Zhang Q, Liu Y, Lin Z-F, Zhang S-X, Sun M-X, Sodmergen. 2010. The levels of male gametic mitochondrial DNA are highly regulated in angiosperms with regard to mitochondrial inheritance. The Plant Cell 22, 2402–2416. Wolfe KH, Li W-H, Sharp PM. 1987. Rates of nucleotide substititution vary greatly between plant mitochondrial, chloroplast and nuclear DNA. Proceedings of the National Academy of Sciences USA 84, 9054–9058. Woodcock CF, Bogorad L. 1970. Evidence for variation in the quantity of DNA among plastids of Acetabularia. Journal of Cell Biology 44, 361–375. Zerges W, Girard-Bascou J, Rochaix JD. 1997. Translation of the chloroplast psbC mRNA is controlled by interactions between its 5’ leader and the nuclear loci TBC1 and TBC3 in Chlamydomonas reinhardii. Molecular and Cell Biology 17, 3440–3448. Zotschke R, Liere K, Börner T. 2007. From seedling to mature plant: Arabidopsis plastidial genome copy number, RNA accumulation and transcription are differentially regulated during leaf development. The Plant Journal 50, 710–722. Downloaded from http://jxb.oxfordjournals.org/ at United Arab Emirates University on June 18, 2015

Why are most organelle genomes transmitted maternally?

The Evolution of Per-cell Organelle Number.

Microbiology. Modern symbionts inside cells mimic organelle evolution.

Mitochondria: an organelle for life.

ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

Endosymbiotic theory for organelle origins.

Genetic regulation of Caenorhabditis elegans lysosome related organelle function.

Upward organelle motility.

Isolation of leaf peroxisomes from Arabidopsis for organelle proteome analyses.

Mechanisms of Polarized Organelle Distribution in Neurons.

Evolution and significance of the Lon gene family in Arabidopsis organelle biogenesis and energy metabolism.

Organelle dynamics. KIF7 organizes cilia.

Passive virus movements with organelle dynamics.

Control of organelle transmission in Chlorophytum.

Proteomics of a fuzzy organelle: interphase chromatin.

Organelle interactions: melanosomes and mitochondria get cozy.

Calcium Homeostasis and Organelle Function in the Pathogenesis of Obesity and Diabetes.

A framework for an organelle-based mathematical modeling of hyphae.

Complete sequences of organelle genomes from the medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids.

Function of metabolic and organelle networks in crowded and organized media.

Organelle dynamics: (P)TEN-ding to mitochondria.

Metabolic Genes within Cyanophage Genomes: Implications for Diversity and Evolution.

Fatty acid metabolism meets organelle dynamics.

Organelle-localized potassium transport systems in plants.