A fragmented metazoan organellar genome: the two mitochondrial chromosomes of Hydra magnipapillata
© Voigt et al; licensee BioMed Central Ltd. 2008
Received: 11 January 2008
Accepted: 26 July 2008
Published: 26 July 2008
Animal mitochondrial (mt) genomes are characteristically circular molecules of ~16–20 kb. Medusozoa (Cnidaria excluding Anthozoa) are exceptional in that their mt genomes are linear and sometimes subdivided into two to presumably four different molecules. In the genus Hydra, the mt genome comprises one or two mt chromosomes. Here, we present the whole mt genome sequence from the hydrozoan Hydra magnipapillata, comprising the first sequence of a fragmented metazoan mt genome encoded on two linear mt chromosomes (mt1 and mt2).
The H. magnipapillata mt chromosomes contain the typical metazoan set of 13 genes for respiratory proteins, the two rRNA genes and two tRNA genes. All genes are unidirectionally oriented on mt1 and mt2, and several genes overlap. The gene arrangement suggests that the two mt chromosomes originated from one linear molecule that separated between nd5 and rns. Strong correlations between the AT content of rRNA genes (rns and rnl) and the AT content of protein-coding genes among 24 cnidarian genomes imply that base composition is mainly determined by mt genome-wide constraints. We show that identical inverted terminal repeats (ITR) occur on both chromosomes; these ITR contain a partial copy or part of the 3' end of cox1 (54 bp). Additionally, both mt chromosomes possess identical oriented sequences (IOS) at the 5' and 3' ends (5' and 3' IOS) adjacent to the ITR. The 5' IOS contains trnM and non-coding sequences (119 bp), whereas the 3' IOS comprises a larger part (mt2) with a larger partial copy of cox1 (243 bp).
ITR are also documented in the two other available medusozoan mt genomes (Aurelia aurita and Hydra oligactis). In H. magnipapillata, the arrangement of ITR and 5' IOS and 3' IOS suggest that these regions are crucial for mt DNA replication and/or transcription initiation. An analogous organization occurs in a highly fragmented ichthyosporean mt genome. With our data, we can reject a model of mt replication that has previously been proposed for Hydra. This raises new questions regarding replication mechanisms probably employed by all medusozoans, and also has general implications for the expected organization of fragmented linear mt chromosomes of other taxa.
Mitochondria were most likely acquired by the common ancestor of eukaryotes [1–3]. Presumably, these organelles originated from incorporated α-proteobacteria and still carry their own, reduced genome . Mitochondrial (mt) genomes show very diverse organizations and are of a very broad range of sizes [3–5]. In comparison to many protists and plants, metazoans possess an even more reduced set of mt genes and fewer non-coding regions . Typical metazoan mt genomes are circular DNA molecules of 16–20 kb [6, 7]. Remarkable exceptions are the linear mt genomes of medusozoan cnidarians (Cnidaria excluding Anthozoa). Linear mt genomes have not been found in other metazoan taxa, but in various other eukaryotes (e.g., [8–12]). The linear structure of cnidarian mt genomes is known from the work of Warrior , who separated the DNA of isolated mitochondria via electrophoresis, as well as from Bridge et al.  and Ender and Schierwater , who applied rnl-probes to electrophoretically separated DNA extracts. Most of the medusozoan mt genomes from these studies were encoded on one ~16 kb molecule, which has been verified by the first two sequences of such linear metazoan genomes (Aurelia aurita (Scyphozoa) , and Hydra oligactis (Hydrozoa) ). However, in some Hydra species, and apparently in some Cubozoa, the mt DNA is divided onto at least two different molecules [13–15]. In the genus Hydra, mt genomes are organized on one ~16 kb molecule or two ~8 kb molecules [13, 14], making this genus an excellent candidate in which to examine changes due to fragmentation of mt genomes from one to two chromosomes. The Hydra oligactis mt genome, a 16.3 kb linear DNA molecule, was published recently . Pont-Kingdon et al.  sequenced a terminal section (3,232 bp) of one of the two mt chromosomes from Hydra vulgaris (as Hydra attenuata), and previous hybridization experiments have shown that in this species all four termini possess a 150–200 bp identical sequence with unknown orientation to one another . By providing the complete mt genome sequence of Hydra magnipapillata, encoded on two mt chromosomes, we now present in detail the organization of such a fragmented linear mt genome from early diverging Metazoa.
To exclude the possibility that other observations in our assemblies originated from methodological artifacts, we conducted additional experimental procedures and tests as follows:
1. PCR experiments
PCR experiments were done with a closely related Hydra species. We obtained specimens of Hydra sp. from the Schulbiologie-Zentrum Hannover. DNA from one polyp was prepared with the Chelex method (protocol as described in ), 1 μl of the undiluted supernatant or 1 μl of a 1:10 dilution was used as template. Phylogenetic analysis with partial cox1 data verified that our Hydra sp. specimen is very closely related to Hydra magnipapillata (see Results).
Primers (Additional file 3) were designed to confirm our bioinformatically derived observations via PCR. The fragments shown in Fig. 1 were amplified and sequenced (some in two overlapping parts, see Additional file 3 for details). Sequences have been submitted to GenBank [GenBank: EU683621–EU683624].
2. Additional local genome assembly experiments
To exclude the possibility that we had amplified a nuclear mt pseudogene (NUMT) of the nd5 and partial cox1 fragment, we started different assemblies with the pipeline originating from blast hits of a 200 bp fragment (100 bp both down- and up-stream of the connection of nd5 and cox1 in the assembly), as well as two assemblies starting from the last 100 bp 3' of nd5, and the first 100 bp of the incomplete copy of cox1. In the first two cases, only one assembly was received, each time consistent with our former assemblies. By starting with 100 bp of the partial cox1, we recovered different assemblies, which were compatible with one chromosomal assembly or the other. In no case did we observe any inconsistencies or any presence of nuclear genes, which would have indicated that the nd5-cox1 arrangement is part of a NUMT.
The H. magnipapillata and Hydra. sp cox1 sequences from our assembly and sequencing were manually aligned with additional sequences from other Hydra and outgroup species available from GenBank in the SeaView editor . The final dataset contained 560 characters. A maximum likelihood analysis was carried out in PAUP* 4.0b10  under a model of nucleotide evolution suggested by the hierarchical likelihood ratio test in Modeltest 3.7 ; for the bootstrap analysis (1,000 replicates) we applied the same model. The dataset was also analyzed with MrBayes v3.1.2 [26, 27] (six substitution rates with a proportion of invariant sites, two runs with eight chains each for 2 million generations with a sample frequency of 100 generations, and a burn-in of 50,000 generations). Parameter stabilization of the chains in MrBayes was monitored with Tracer 1.4 , and convergence of chains was examined with the diagnostics provided by the AWTY server [29, 30].
Base compositions of cnidarian mt genomes
Sequences of 23 additional cnidarian genomes were downloaded from GenBank  (see Additional file 4 for taxa and accession numbers). The sequences of the 13 respiratory chain protein genes shared between all 24 mt genomes and the sequences of rns and rnl were extracted from the GenBank format using the Artemis software v.9 . In some mt genomes the rRNA genes were not entirely annotated in their full length. We therefore considered the non-coding regions around the apparently too small genes as rRNAs. The corresponding taxa and positions in each sequence were: Nematostella sp. [GenBank: NC_008164] (rns: 5054..6171; rnl: 10342..12484); Mussa angulosa [GenBank: NC_008163] (rns: 6901..8038; rnl: 15327..17170); Astrangia sp. [GenBank: NC_008161] (rns: 6899..7797; rnl: 12982..14681). The AT contents of rRNAs and protein codon positions of the mt genomes are shown in Additional file 4.
Genes, base composition and codon usage
The two chromosomes of the H. magnipapillata mt genome each carry one rRNA gene (mt1:rnl; mt2: rns). Each of the assembled contigs of mt1 and mt 2 is represented by > 7,000 single sequence reads from the trace archive (Additional file 1). Our consensus sequence for mt1 is 8,194 bp long. This matches the length reported by Bridge et al.  for this H. magnipapillata mt chromosome. The sequence of mt2 is shorter (7,686 bp).
The H. magnipapillata mt genome includes 13 protein-coding genes of the respiratory chain usually found in other Metazoa. mt1 contains 6 protein-coding genes, rnl and two tRNA genes; mt2 contains 7 protein-coding genes, rns and one tRNA gene (Fig. 1A). All genes are unidirectionally encoded on each of the two molecules and densely arranged along the chromosomes. As in H. oligactis, the longest non-coding intergenic region is 52 bp between cox3 and nd2 . Otherwise, subsequent genes are separated by 0–5 bp or overlap for up to 10 bp (in nd6-nd3 and nd1-nd4).
Like many other Cnidaria [16, 17, 32–34], the H. magnipapillata mt genome possesses only the two tRNA genes for methionine (trnM; CAU) and tryptophan (trnW; UCA). trnW is only found on mt1, whereas identical copies of trnM are present on both chromosomes (Fig. 1B).
Gene arrangement and inverted terminal repeats
Compared to the gene arrangement of A. aurita and H. oligactis, only a few changes can be observed in H. magnipapillata. Neglecting the positions of tRNAs, two blocks (cox2, atp8, atp6, cox3, nd2, nd5 and rns; nd6, nd3, nd4L, nd1, nd4, cob) of genes are identical across the three genomes, occurring on mt1 or mt2, respectively, in H. magnipapillata (Fig. 1A). The mt genomes of H. oligactis and of H. magnipapillata are entirely alignable and display a sequence divergence of 12.3% (excluding the terminal chromosome structures; see below).
As mentioned before, we found 191–196 bp of ITR at both ends of mt1 and mt2. In the linear mt genomes of H. oligactis and A. aurita, ITR were also present but were longer (H. oligactis: 1,488 bp; A. aurita: 471 bp, [16, 17] assuming symmetry for unsequenced ends). Unlike ITR in Aurelia , ITR in H. magnipapillata have a higher GC content than the rest of the molecule (52.2% GC in ITR vs. 25.2% GC in 5' IOS [see below], 27.6% GC in 3' IOS [see below] and a mean of 22.5% GC for all remaining regions). We found that a smaller part of 3' cox1 (54 bp) is included in all ITR of H. magnipapillata. Probably because the 3' end of cox1 is not very conserved, Pont-Kingdon et al.  missed this feature in their mt1 fragment of H. vulgaris. The ITR regions of H. oligactis contain a larger cox1 fragment (one non-functional copy at the 5' end, functional cox1 at 3' end, Fig. 1A). The remaining sequenced 3' region of ITR in H. oligactis is very similar to those found in H. magnipapillata and H. vulgaris (Fig. 1C), but longer. Between H. magnipapillata and H. vulgaris, the major difference is that a stretch of Gs (31 in H. vulgaris) is significantly shorter in H. magnipapillata (11–16 at the homologous region).
In H. magnipapillata mt1 and mt2, we found additional identical sequences at the 5' and 3' ends following (at the 5' ends) and preceding (at the 3' ends) the ITR. We refer to those regions as identically oriented sequences (5' and 3' IOS, Fig. 1B). After the ITR, the 5' IOS of both molecules contain identical copies of non-coding DNA and trnM. At the 3' IOS we found a larger partial copy of the 5' region of cox1 on mt1. As a consequence of this arrangement, mt1 and mt2 share 310 bp (ITR+5' IOS) at the 5' end and 436 bp (3' IOS+ITR) at the 3' end, giving both molecules a specific orientation.
Using PCR experiments with the closely related Hydra sp., we verified the following arrangements initially observed in the H. magnipapillata sequences (compare Fig. 1A): (i) the presence and orientation of the ITR at all four chromosome ends could be shown, as well as the presence of partial cox1 sequences in the ITR; (ii) identical regions are shared at the 5' and 3' end, respectively, between mt1 and mt2 adjacent to the ITR; and (iii) within the latter regions, the 5' motif contains trnM, which therefore appears in two copies in the genome, and a larger sequence of cox1 forms the shared 3' motif of mt1 and mt2.
Linear mt genomes and fragmentation of mt chromosomes in Cnidaria
Linearity of mt genomes seems to have evolved once after the divergence of Medusozoa from Anthozoa. Fig. 3A summarizes the results of different studies [13, 15–17], mapped on a cnidarian phylogeny . A fragmentation of mt genomes has been reported from several Hydra species (Hydrozoa) [13, 14] and Cubozoa . Uncertainties remain for Cubozoa: Bridge et al.  studied the same cubozoan species Carybdea marsupialis as Ender and Schierwater , but reported a single ~16 kb linear mt genome, while in the more recent work, a ~4 kb fragment was shown to carry the rnl gene. Because Ender and Schierwater  were able to repeat the experiments with different DNA isolates of C. marsupialis and obtained concordant results from an additional cubozoan species (Tripedalia cystophora), an experimental error seems unlikely. However, their conclusion of four equally-sized mt chromosomes in Cubozoa is not directly supported by their identification of a 4 kb chromosome carrying rnl. Alternatively, one could assume the presence of a single ~12 kb mt counterpart, as indicated in Fig. 3A. Such an arrangement is possible, e.g., if rnl and cox1, the two genes that are encoded in different orientation to the other mt genes in A. aurita , were encoded in one chromosome in Cubozoa, and the remaining genes on a second chromosome.
However, given the available data it seems reasonable to assume that fragmented linear genomes occur in both Cubozoa and Hydrozoa (in some members of the genus Hydra). This suggests from an evolutionary perspective that the mt genome in the common ancestor of Medusozoa was linear and then independently split into different chromosomes in Hydra (Fig. 3B), and in at least some Cubozoa (compare Fig. 3A).
A possible mechanism for the origin of linear chromosomes from a circular molecule is the integration of one or more resolution elements . The circular DNA molecule would be split into one or more linear molecules with identical ends. In Medusozoa, the processes of linearization and the split of one linear into two linear chromosomes were obviously different processes as shown in the phylogenetic trees (Fig. 3). The linearization, possibly occurring in the last common ancestor of medusozoans, seems to have preceded the splitting of the chromosomes by a long time. If the ancestral linear mt chromosome of Medusozoa originated by introduction of a resolution element, one probably would not expect to observe its original motifs, which would occur as identical repeats at the two ends of the linear molecule . Indeed, the ends of linear medusozoan mt chromosomes have inverted terminal motifs (the ITR), instead of direct repeats. The splitting of ancestral linear mt chromosomes as in H. magnipapillata (and possibly Cubozoa) happened much later in evolutionary history, contradicting the view that the two or more linear mt chromosomes in Medusozoa directly originated from one circular DNA molecule.
Fragmented mt genomes are present in various eukaryotic taxa, e.g., in dinoflagellates [38, 39], Ichthyosporea  and Fungi . In Metazoa, fragmented mt genomes are known from the genera Globodera (Nematoda [41–43]), Dicyema (Mesozoa ) and the rotifer Brachionus plicatilis , but unlike in H. magnipapillata, in these taxa the genomes are encoded on several small circular molecules. The mt chromosomal organization observed in H. magnipapillata supports the hypothesis of an ancestral, linear chromosome in Hydra (Fig. 3B), as represented by the mt genome of H. oligactis , which has been split in two between nd5 and rns.
Function of ITR and IOS
Warrior  already suggested the presence of identical terminal sequences on both chromosomes of H. vulgaris. We now show that these ends are arranged as ITR on mt1 and mt2, as in other medusozoans [16, 17]. In H. oligactis, which in the phylogenetic tree branches off before Hydra species carrying two mt DNA molecules (Fig. 3B), the single linear mt chromosome has ITR containing a large copy of the 5' end of cox1. Only the ITR at the 3' end has been completely sequenced . Based on our findings in H. magnipapillata, we predict that the unsequenced 5' end is almost identical to the 3' motif (Fig. 1), and we expect that about 150 bp remain unsequenced on the 5' end (in contrast to the 65 bp that have been proposed ). In Hydra, partial copies of cox1 play a crucial role as part in ITR regions at the chromosome ends (Fig. 1, ). The ITR in H. magnipapillata contains only a short sequence of the 3' end of cox1 (54 bp, compared to the 1,284 bp in H. oligactis), suggesting that large parts of the cox1 copies were lost. A simultaneous duplication of 5' ITR (containing the already shortened partial cox1 copy) and the 5' IOS motif seems likely to have occurred in the process of chromosome splitting. In this case, the longer cox1 copy (containing additional 240 bp of cox1) is a duplication of the functional cox1 of the original 5' end of a single mt chromosome (Fig. 1A).
ITR of linear mt molecules are present in other taxa besides medusozoans, e.g., in yeasts (e.g., ) and in the green algae Chlamydomonas reinhardtii . Furthermore, in the green algae Polytomella parva, identical ITR are present at all ends of the two linear mt chromosomes , similar to what we observe in H. magnipapillata. We report 5' and 3' IOS as an additional shared feature of the two mt chromosomes. Interestingly, such an arrangement of ITR and 5' and 3' IOS is also seen in another, highly fragmented eukaryotic mt genome. In the ichthyosporean Amoebidium parasiticum, mt genes are distributed over several hundred different chromosomes, each of which also possesses ITR and 5' and 3' IOS .
Pont-Kingdon et al.  speculated that there may be a role for transcription initiation at the 240 bp 5' of trnM, which they found in their H. vulgaris (as H. attenuata) partial mt1 sequence. Considering that transcription initiation within the ITR would result in energetically expensive nonsense transcripts (since all genes are encoded on only one strand), transcription is more likely to start in the adjacent, non-coding regions of the 5' IOS. In H. magnipapillata and H. vulgaris this region within the 5' IOS is 40 bp long and lies between the cox1 copy and trnM (Fig. 1B). In H. oligactis, the non-coding region between the ITR and trnM is only 6 bp. However, a striking sequence similarity can be observed near trnM between H. oligactis and H. vulgaris (with the same sequence in this region as H. magnipapillata) . There is a 14-bp motif (TTATTTRRTCTTCT) that is shared between the species and differs by the last 3 bp from the 3' ITR+3 bp counterpart in H. oligactis. This motif might be involved in transcription initiation. If so, the difference in the very last 3 bp between the 5' end and its counterpart on the reverse strand in the ITR of H. oligactis prevents a functional transcription signal on the non-coding strand in this species. A crucial function for transcription initiation would explain selective pressure for maintaining the 5' IOS of both molecules after the ITR in H. magnipapillata. All mt chromosomes from Amoebidium parasiticum that contain coding genes are transcribed from 5' IOS to 3' IOS, as in H. magnipapillata . This observation led Burger et al.  to the conclusion that the IOS in Amoebidium are responsible for transcription initiation (5' IOS) and termination (3' IOS). While in H. magnipapillata we expect the same function for 5' IOS, the role of the additional partial cox1 copy within the 3' IOS of mt1 and mt2, if any, remains unknown; considering that the end of cox1 is part of the ITR, transcription can only be terminated in ITR and not in the 3' IOS. The sequence homologies of ITR and IOS within or between mt1 and mt2 are probably not the result of a relatively recent origin from ancestral sequences, as a first duplication of partial cox1 is already observed in H. oligactis and therefore predates the separation process. The substitutions between ITR (partial cox1) of the two species are found in all ITR copies in each mt genome. Considering this and the fact that similar arrangements are found in other eukaryotes [8–12, 16], it seems more likely that concerted evolution maintains the almost identical sequences, probably caused or influenced by the yet unknown mt genome replication mechanism. Terminal sequences of linear DNA molecules play a crucial role in mt replication . The main problem in the process of linear chromosome replication is the maintenance of the 5' ends. In nuclear (nc) chromosomes this is normally achieved by telomerase, an enzyme that adds short sequence motifs in tandem repeats at the end of each molecule to compensate for loss at the 5' end that occurs in each replication cycle . Consequently, in Hydra as in most Metazoa, the motif (TTAGGG)n is found at the end of nc chromosomes . The termini of Hydra mt chromosomes are much more complex, and their maintenance during replication is not yet understood but is most likely telomerase independent . Warrior  suggested an mt replication mechanism for the two H. vulgaris mt chromosomes similar to that of T7 bacteriophages. His conclusion was based upon observations from hybridization experiments, which showed the presence of identical terminal sequences that he assumed to have the same orientation at the 5' and 3' ends. According to this model, intermediate concatamers are formed, and via ligation, site-specific nicking and elongation, the 5' ends are finally filled. Based on our data we can reject this model, because we showed that the terminal sequences in H. magnipapillata are inverted (ITR) and therefore do not allow the necessary concatamerization in the proposed way. Similarly, ephemeral circularization as in the phage lambda is not possible when terminal sequences are not direct repeats, but inverted.
Different replication mechanisms for linear chromosomes have been reported or proposed (for review, see ). Solutions for maintaining the terminal structure in sequences with ITR include (a) covalently bound proteins, which also could serve as primers for a 'racket frame' replication (e.g., in linear mt chromosomes of plants and fungi or adenoviruses [48, 49]), (b) 5' and 3' ends of chromosomes that are connected by a hairpin-loop (e.g., in some yeasts [9, 48]) and (c) single-stranded 3' overhangs (e.g., in Chlamydomonas reinhardtii ). Warrior  showed that the first two possibilities are not realized in H. vulgaris. The mt-replication mechanism in Chlamydomonas requires an internal repeat of the single-stranded 3' overhangs . We cannot entirely rule out the existence of short single-stranded 3' overhangs, as it is possible they might have been missed due to our methods. The outermost sequence at least cannot be part of a repeat motif, as our PCR amplification of Hydra sp. did not yield fragments of different sizes. Furthermore, neither in mt1 of H. vulgaris nor in the mt genome of H. oligactis were additional sequences or repeats found [13, 17]. Therefore, although a similarity to the mt replication of C. reinhardtii cannot be excluded, we find that mechanisms for linear mt chromosome replication are too diverse and that too many details are still unknown [4, 48] for us to draw further conclusions about the replication process in H. magnipapillata from the presence of the ITR alone. Considering that ITR are a shared feature among all three available sequences of medusozoan mt genomes (H. oligactis [16, 17], A. aurita [16, 17] and H. magnipapillata), it is very likely that the mechanisms for mt replication are similar in all medusozoans and are still the same after the fragmentation of the mt genome. Keeping in mind that similar arrangements of ITR and IOS are found in Amoebidium parasiticum, the mt replication mechanisms of H. magnipapillata and Medusozoa are probably not unique among eukaryotes.
The H. magnipapillata mt genome represents the first complete sequence of a linear metazoan mt genome that consists of two separate molecules. The gene arrangements and our phylogenetic analysis suggest that mt1 and mt2 originated from an ancestral linear mt genome, as found in H. oligactis, that at some point divided in two between nd5 and rns (Figs. 1 and 3). Of most interest is the organization at the ends of the two mt chromosomes (Fig. 1). We show that H. magnipapillata has ITR, which include a part of cox1 (at the 3' ITR of mt2) or partial copies of the 5' end of cox1 (all other ITR). We conclude that mechanisms for mt replication in Hydra species are different from the previously proposed ones and probably are shared among all medusozoans. In addition to ITR, both mt chromosomes of H. magnipapillata have identical motifs on their 5' and 3' ends, called respectively the 5' IOS and 3' IOS (Fig. 1). The 5' IOS includes trnM and a non-coding region, including a motif that may play a role in transcription initiation. The 5' IOS is probably the result of a duplication during the separation process of a single ancestral mt chromosome. The organization of the ITR and 5' and 3' IOS is not unique among eukaryotes with fragmented linear mt genomes. ITR most likely play a role in mt replication, while the duplication of the 5' end of an single ancestral linear and unidirectionally-encoded mt chromosome (with the presence of 5' IOS) and its concerted evolution ensure that transcription of all mt genes is maintained after fragmentation of linear mt chromosomes. A similar arrangement of ITR and IOS regions can therefore be expected in the apparently fragmented mt genomes of Cubozoa and other eukaryotes with two or more linear mt DNA molecules.
This work was financially supported by the German Research Foundation (DFG, Projects Wo896/3-1, 3 & Wo896/6-1) and is a contribution from the DFG Priority Programme SPP1174 "Deep Metazoan Phylogeny". D.E. acknowledges financial support from the European Union under a Marie Curie outgoing fellowship (MOIF-CT-2004 Contract No. 2882). All authors acknowledge the J. Craig Venter Institute for providing H.magnipapillata WGS traces via NCBI's trace archive, and the National Human Genome Research Institute for funding the H. magnipapillata genome project. We thank Bernie Degnan and Ben Woodcroft (School of Integrative Biology, The University of Queensland, Brisbane) for providing access to their 'Reefedge' pipeline for local genome assembly and the Schulbiologiezentrum Hannover for providing Hydra specimens for our PCR experiments. OV thanks Catherine Vogler for help with R and many useful discussions and remarks on the manuscript.
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