Complete nucleotide sequences of the nuclear pseudogenes for cytochrome oxidase subunit I and the large mitochondrial ribosomal RNA in the sea urchin Strongylocentrotus purpuratus

Genetic Variation in the Atlantic Bobtail Squid-Vibrio Symbiosis From the Galician Rías

Symbiotic marine bacteria that are transmitted through the environment are susceptible to abiotic factors (salinity, temperature, physical barriers) that can influence their ability to colonize their specific hosts. Given that many symbioses are driven by host specificity, environmentally transmitted symbionts are more susceptible to extrinsic factors depending on conditions over space and time. In order to determine whether the population structure of environmentally transmitted symbionts reflects host specificity or biogeography, we analysed the genetic structure of Sepiola atlantica (Cephalopoda: Sepiolidae) and their Vibrio symbionts (V. fischeri and V. logei) in four Galician Rías (Spain). This geographical location is characterized by a jagged coastline with a deep-sea entrance into the land, ideal for testing whether such population barriers exist due to genetic isolation. We used haplotype estimates combined with nested clade analysis to determine the genetic relatedness for both S. atlantica and Vibrio bacteria. Analyses of molecular variance (AMOVA) were used to estimate variation within and between populations for both host and symbiont genetic data. Our analyses reveal a low percentage of variation among and between host populations, suggesting that these populations are panmictic. In contrast, Vibrio symbiont populations show certain degree of genetic structure, demonstrating that the hydrology of the rías is driving bacterial distribution (and not host specificity). Thus, for environmentally transmitted symbioses such as the sepiolid squid-Vibrio association, abiotic factors can be a major selective force for determining population structure for one of the partners.

Phylogeographic patterns in the Philippine archipelago influence symbiont diversity in the bobtail squid-Vibrio mutualism

Marine microbes encounter a myriad of biotic and abiotic factors that can impact fitness by limiting their range and capacity to move between habitats. This is especially true for environmentally transmitted bacteria that cycle between their hosts and the surrounding habitat. As geologic history, biogeography, and other factors such as water temperature, salinity, and physical barriers can inhibit bacterial movement to novel environments, we chose to examine the genetic architecture of Euprymna albatrossae (Mollusca: Cephalopoda) and their Vibrio fischeri symbionts in the Philippine archipelago using a combined phylogeographic approach. Eleven separate sites in the Philippine islands were examined using haplotype estimates that were examined via nested clade analysis to determine the relationship between E. albatrossae and V. fischeri populations and their geographic location. Identical analyses of molecular variance (AMOVA) were used to estimate variation within and between populations for host and symbiont genetic data. Host animals demonstrated a significant amount of variation within island groups, while symbiont variation was found within individual populations. Nested clade phylogenetic analysis revealed that hosts and symbionts may have colonized this area at different times, with a sudden change in habitat. Additionally, host data indicate restricted gene flow, whereas symbionts show range expansion, followed by periodic restriction to genetic flow. These differences between host and symbiont networks indicate that factors "outside the squid" influence distribution of Philippine V. fischeri. Our results shed light on how geography and changing environmental factors can impact marine symbiotic associations at both local and global scales.

Numts: an impediment to DNA barcoding of Polyclinids, Tunicata

The mitochondrial cytochrome c oxidase subunit I (COI) gene, a widely accepted molecular marker for species identification and classification, has been questioned because of the presence of Numts. In this study we found the presence of Numts in the COI chromatogram of two tunicates, Polyclinum indicum and Polyclinum madrasensis belonging to the genus Polyclinum. Numts were also present in our sequence (Accession Number: KJ944391) and in other sequences belonging to genus Polyclinum in the GenBank record. The GeneBank database of genus Polyclinum contains COI-like sequences and COI pseudogenes, but no record of COI gene from Polyclinids. The prevalence of Numts in Polyclinids belonging to Tunicata, is an impediment to DNA barcoding studies of Polyclinum species.

A phylogeny of the oil bee tribe Ctenoplectrini (Hymenoptera: Anthophila) based on mitochondrial and nuclear data: evidence for early Eocene divergence and repeated out-of-Africa dispersal

The bee tribe Ctenoplectrini, with two genera, comprises nine species in tropical Africa and ten in Asia and Australia. Most of them collect floral oil, pollen, and nectar from Cucurbitaceae, but three species are thought to be cleptoparasites. The unusual morphology of Ctenoplectrini has made it difficult to infer their closest relatives, in turn preventing an understanding of these bees' geographic and temporal origin. We used two mitochondrial and two nuclear markers (4741 nucleotides) generated for most of the species to test the monophyly of the tribe, its relationships to other Apidae, and its biogeographic history. Ctenoplectrini are strongly supported as monophyletic and closest to the Long-horned bees, Eucerini. The presumably cleptoparasitic species form a clade (Ctenoplectrina) that is sister to the remaining species (Ctenoplectra), confirming the independent evolution of cleptoparasitism in this tribe. Tree topology and molecular dating together suggest that Ctenoplectrini originated in Africa in the Early Eocene and that Ctenoplectra dispersed twice from Africa to Asia, sometime in the Late Eocene, 30-40 my ago, from where one species reached the Australian continent via Indonesia and New Guinea in the mid-Miocene, c. 13 my ago. Dry and cool mid-Miocene climates also coincide with the divergence between Ctenoplectra bequaerti from West Africa and Ctenoplectra terminalis from East and South Africa, perhaps related to fragmentation of the equatorial African rainforest belt.

Origin of intra-individual variation in PCR-amplified mitochondrial cytochrome oxidase I of Thrips tabaci (Thysanoptera: Thripidae): mitochondrial heteroplasmy or nuclear integration?

The mitochondrial genome is increasingly being used as a species diagnostic marker in insects. Typically, genomic DNA is PCR amplified and then analysed by restriction analyses or sequencing. This analysis system may cause some serious problems for molecular diagnosis. Besides the errors introduced by the PCR process, mtDNA sequence variation of amplified fragments may originate from mtDNA heteroplasmy or from nuclear integrations of mtDNA fragments, both of which have been shown to occur in insects. Here we document abundant variation in PCR-amplified sequences of the mitochondrial cytochrome oxidase I gene of Thrips tabaci. We confirm that the most common haplotype is of mitochondrial origin. Some of the observed mutations were introduced by the amplification process. However, the occurrence of some haplotypes at elevated frequencies indicates that within-individual variation of the respective fragment exists at low levels in T. tabaci. The frequencies of these sequences are too low to negatively affect mtDNA-based molecular diagnosis of T. tabaci. The possible origin of these variant haplotypes is discussed.

Regulation of cytochrome c oxidase subunit 1 (COX1) expression in Cryptococcus neoformans by temperature and host environment

In the study of differential gene expression of Cryptococcus neoformans, a transcript of COX1 (cytochrome oxidase c subunit 1) was identified in a serotype A strain. The transcript was upregulated at 37 degrees C compared to 30 degrees C and expressed by yeasts infecting the central nervous system. Northern analysis of COX1 from the serotype A strain revealed two polycistronic transcripts, a temperature-upregulated 2.3 kb transcript and a 1.9 kb transcript that was not affected by temperature. In contrast, COX1 in a serotype D strain showed only a 1.9 kb polycistronic transcript plus a 1.6 kb monocistronic message, and temperature had no effect on the transcripts. The sequence of COX1 revealed similar coding regions between the two strains, but the serotype D strain had five introns whereas no introns were found in the serotype A strain. The serotype D strain had reduced growth rates compared to the serotype A strain at 37 degrees C, but in an AD hybrid strain the serotype D COX1 gene could support efficient high temperature growth. These studies have revealed mitochondrial molecular differences between serotype A and D strains which show evolutionary divergence. It will be important to determine whether differences in mitochondrial structure and function can influence cryptococcosis.

A putative RNA editing from U to C in a mouse mitochondrial transcript

Recently, we isolated and characterized a new mouse mitochondrial RNA molecule containing the mitochondrial 16S RNA plus 121 nt joined to the 5' end of the RNA. This fragment arises from the L strand of the same gene and we have named this transcript chimeric RNA. At position 121 of the RNA there is a C, which, according to the sequence of the mitochondrial 16S RNA gene, should be a U. We hypothesized that this RNA is synthesized having a U at position 121, which is later substituted to a C by a putative editing reaction. Based on the presence of sites for the restriction endonucleases RsaI and Fnu4HI around position 121, both forms of the RNA were detected in mouse tissues. To confirm the presence of the non-edited and putative edited RNA, a fragment containing the first 154 nt of the RNA was amplified by RT-PCR and cloned. The substitution of U for C was demonstrated by sequencing these clones. In vitro transcription experiments demonstrated that the substitution of U for C is not due to artifact of amplification or cloning. Moreover, in mitochondria from testis only the non-edited form was found. This, together with other experimental evidence, demonstrated that the base substitution was not due to polymorphism of the mitochondrial 16S RNA gene. This is the first demonstration of a substitution reaction from U to C in a mammalian mitochondrial transcript.

Recombination among multiple mitochondrial pseudogenes from a Passerine genus

PCR products of a fragment of the mitchondrial protein coding subunit 5 of NADH-dehydrogenase (ND5) from eight individuals representing five species of the South American bird genus Conirostrum were cloned. The 130 clones, which were subsequently sequenced, constituted 55 different sequences. Due to the observed differences in substitution patterns 58% of the cloned sequences were identified as pseudogenes. Recombination could be traced in 19% of the inferred nuclear pseudogenes, but this figure probably represents a significant underestimation of the factual recombination events. The nonrecombined pseudogenes consisted of multiple haplotypes found to diverge from 1 to 16% from the mitochondrial gene. The number of mitochondrial nuclear copies and their apparent frequent recombination suggest that pseudogenes constitute a serious potential risk in confounding phylogenetic studies and population genetic analysis.

A novel chimeric mitochondrial RNA localized in the nucleus of mouse sperm

Six identical cDNA clones corresponding to an RNA of 1685 nucleotides that is enriched in mouse sperm compared with testis were isolated from a mouse testis cDNA library. The sequence of these clones corresponds to the 16S mitochondrial RNA plus an inverted repeat of 120 bp covalently joined to the 5' end of the RNA. By RT-PCR, it was demonstrated that this transcript, referred to as chimeric RNA, was present in mouse sperm, testis, liver, kidney, brain, and spleen. The absence of an equivalent sequence in mitochondrial DNA or as a mitochondrial pseudogene in total DNA extracted from sperm, testis, and somatic tissues suggests that the chimeric RNA is a post-transcriptional product, maybe resulting from a trans splicing reaction. The chimeric RNA was found by RT-PCR in total RNA extracted from purified sperm heads. This result was confirmed by in situ hybridization, which showed clear staining of the sperm nucleus with probes corresponding to sequences of the mitochondrial 16S RNA and the inverted repeat.

Nuclear pseudogenes of mitochondrial DNA as a variable part of the human genome

Novel pseudogenes homologous to the mitochondrial (mt) 16S rRNA gene were detected via different approaches. Eight pseudogenes were sequenced. Copy number polymorphism of the mtDNA pseudogenes was observed among randomly chosen individuals, and even among siblings. A mtDNA pseudogene in the Y-chromosome was observed in a YAC clone carrying only repetitive sequence tag site (STS). PCR screening of human yeast artificial chromosome (YAC) libraries showed that there were at least 5.7 x 10(5) bp of the mtDNA pseudogenes in each haploid nuclear genome. Possible involvement of the mtDNA pseudogenes in the variable part of the human nuclear genome is discussed.

Multiple independent transpositions of mitochondrial DNA control region sequences to the nucleus

Transpositions of mtDNA sequences to the nuclear genome have been documented in a wide variety of individual taxa, but little is known about their taxonomic frequency or patterns of variation. We provide evidence of nuclear sequences homologous to the mtDNA control region in seven species of diving ducks (tribe Aythyini). Phylogenetic analysis places each nuclear sequence as a close relative of the mtDNA haplotypes of the specie(s) in which it occurs, indicating that they derive from six independent transposition events, all occurring within the last approximately 1.5 million years. Relative-rate tests and comparison of intraspecific variation in nuclear and mtDNA sequences confirm the expectation of a greatly reduced rate of evolution in the nuclear copies. By representing mtDNA haplotypes from ancestral populations, nuclear insertions may be valuable in some phylogenetic analyses, but they also confound the accurate determination of mtDNA sequences. In particular, our data suggest that the presumably nonfunctional but more slowly evolving nuclear sequences often will not be identifiable by changes incompatible with function and may be preferentially amplified by PCR primers based on mtDNA sequences from related taxa.

Highly conserved nuclear copies of the mitochondrial control region in the desert locust Schistocerca gregaria: some implications for population studies

Animal mitochondrial DNA has proved a valuable marker in intraspecific systematic studies. However, if nucleotide sequence heterogeneity exists at the individual level, its usefulness will be much reduced. The study demonstrates that the presence of highly conserved non-coding mitochondrial sequences in the nuclear genome of Schistocerca gregaria greatly impairs the use of mtDNA in population genetic studies. Caution is called for in other organisms; and it seems necessary to check for conserved nuclear copies of mitochondrial sequences before launching into a large scale analysis of populations using mtDNA as a genetic marker. Experimental procedures are suggested for this purpose.

Multi-copy nuclear pseudogenes of mitochondrial DNA reveal recent acute genetic changes in the human genome

Four nuclear pseudogenes homologous to the 10031-10195-bp region of the human mitochondrial genome were detected by constant denaturant capillary electrophoresis. Among them, one pseudogene is present as at least five copies in each cell, in accordance with our previous observations of multi-copy mitochondrial DNA pseudogenes. The presence of multiple identical copies of pseudogenes suggests that the human genome underwent a series of genetic changes, including gene amplifications, very recently in evolutionary history, i.e., within the last 390000 years.

Evolutionary trail of the mitochondrial genome as based on human 16S rDNA pseudogenes

In the course of studies on mutations in human mitochondrial (mt) DNA, we have uncovered and sequenced four new nuclear pseudogenes corresponding to bp 2457-2657 of the mt 16S rDNA. The four genes and their homologies with human mtDNA are E2 (62.4%), K10 (74.4%), E1 (84.6%) and LE6 (93.2%). When these five pseudogene sequences and another previously reported pseudogene sequence are compared with each other, they display what appears to be an ordered series of steps from a hypothetical common ancestor. The sequence of the hypothetical ancestor closely resembles that found in a wide variety of present-day mammalian mt genomes. The pseudogene sequences suggest an evolutionary trail of mt mutation dominated by base pair transitions punctuated by integration into the nuclear genome. Once integrated into the nuclear genome, the pseudogenes appear to follow the distinctive nuclear mutational pathway in which GC to AT transitions predominate and CpG sequences are preferentially eliminated.

Do ribosomes regulate mitochondrial RNA synthesis?

The levels of different classes of mitochondrially encoded transcripts are developmentally regulated in sea urchin embryos, as a result of selection between mutually exclusive synthetic pathways. I propose a simple model to explain these observations, based on a dual role for mitochondrial ribosomes and translation factors in RNA synthesis as well as in translation. This effect may be exerted either at the transcriptional or post-transcriptional level (or both), and is potentially generalizable to mammalian mtDNA and to other systems.

Mutually exclusive synthetic pathways for sea urchin mitochondrial rRNA and mRNA

The structure and abundance of mitochondrial transcripts in sea urchin embryos were investigated by a combination of RNA blot-hybridization, S1 mapping, and primer extension assays. Between the egg and blastula stages, the relative abundance of mitochondrial rRNAs declined slightly, while that of mitochondrial mRNAs increased up to 10-fold. Fine mapping of the termini of the rRNAs and of the adjacent transcripts indicated that, although they appeared to be butt-joined at their 5' ends to the upstream transcripts, tRNA-Phe 5' to the small subunit (12S) rRNA and NADH dehydrogenase subunit 2 mRNA 5' to the large subunit (16S) rRNA, respectively, their 3' ends were found to overlap the 5' ends of the downstream transcripts. 12S rRNA was found to extend 7 to 13 nucleotides into the sequence of tRNA-Glu; 16S rRNA was shown to terminate 3 to 5 nucleotides inside the coding region of cytochrome oxidase subunit 1 (COI) and 8 to 10 nucleotides from the mapped 5' end of COI mRNA. The rRNAs and the downstream transcripts must therefore be synthesized by distinct pathways, either by alternative processing of the same primary transcript(s) or by processing of different precursors. In either case, the events which select the ribosomal 3' ends preclude the production of functional transcripts of the downstream genes from the same precursor molecule. No developmental alterations in transcript structure were detected. We propose that mitochondrial RNA levels are regulated in early development by the selection of alternate and mutually exclusive RNA-processing pathways.

Conserved tRNA gene cluster in starfish mitochondrial DNA

Partial sequencing of mtDNA from four long-diverged species of starfish reveals the existence of a conserved cluster of 13 tRNA genes, organized in a manner similar to that of the tRNA cluster of sea urchin mtDNA, but located at a position distant from the presumed replication origin. These findings suggest that a clustered organization of tRNA genes may have been present in the ancestral mitochondrial genome, and raise the possibility that tRNAs may have catalyzed the dispersal rather than the accumulation of the genes which encode them.

Mutually exclusive synthetic pathways for sea urchin mitochondrial rRNA and mRNA

The structure and abundance of mitochondrial transcripts in sea urchin embryos were investigated by a combination of RNA blot-hybridization, S1 mapping, and primer extension assays. Between the egg and blastula stages, the relative abundance of mitochondrial rRNAs declined slightly, while that of mitochondrial mRNAs increased up to 10-fold. Fine mapping of the termini of the rRNAs and of the adjacent transcripts indicated that, although they appeared to be butt-joined at their 5' ends to the upstream transcripts, tRNA-Phe 5' to the small subunit (12S) rRNA and NADH dehydrogenase subunit 2 mRNA 5' to the large subunit (16S) rRNA, respectively, their 3' ends were found to overlap the 5' ends of the downstream transcripts. 12S rRNA was found to extend 7 to 13 nucleotides into the sequence of tRNA-Glu; 16S rRNA was shown to terminate 3 to 5 nucleotides inside the coding region of cytochrome oxidase subunit 1 (COI) and 8 to 10 nucleotides from the mapped 5' end of COI mRNA. The rRNAs and the downstream transcripts must therefore be synthesized by distinct pathways, either by alternative processing of the same primary transcript(s) or by processing of different precursors. In either case, the events which select the ribosomal 3' ends preclude the production of functional transcripts of the downstream genes from the same precursor molecule. No developmental alterations in transcript structure were detected. We propose that mitochondrial RNA levels are regulated in early development by the selection of alternate and mutually exclusive RNA-processing pathways.

Nucleotide sequence and gene organization of sea urchin mitochondrial DNA

The 15,650 base-pair mitochondrial genome of the sea urchin Strongylocentrotus purpuratus has been cloned and sequenced. It exhibits a novel organization that suggests the primacy of post-transcriptional gene regulation. The same 13 polypeptides, two rRNAs and 22 tRNAs are encoded as in other animal mitochondrial DNAs, but are organized with extreme economy; non-coding information between genes is almost completely absent, some stop codons are generated post-transcriptionally and tRNA sequences are interspersed between only a minority of other structural genes. The genome uses a variant genetic code, in which AAA specifies asparagine, ATA isoleucine, TGA tryptophan and AGN serine, and has an unusual pattern of codon bias. The order of genes shows several differences from that of vertebrates. The genes for the large (16 S) ribosomal RNA and for NADH dehydrogenase subunit 4L (ND4L) are in different positions, located respectively between those encoding ND2 and cytochrome oxidase subunit I (COI) and between COI and COII. This organization is conserved amongst at least four regular echinoids diverging by some 225 million years. Most tRNA genes are also in different positions. The only long unassigned sequence in the genome (121 base-pairs) is located within a cluster of 15 tRNA genes. It contains elements resembling some of those found in the displacement (D) loop of vertebrate mtDNAs, notably polypurine/polypyrimidine tracts that may play a role in regulating transcription and the initiation of replication. The separation of the ribosomal RNA genes from each other and from the putative control region imposes special demands on the transcription of the genome.

A novel gene order in the Paracentrotus lividus mitochondrial genome

The mitochondrial DNA (mtDNA) from Paracentrotus lividus (sea urchin) eggs, a circular molecule of about 15,500 bp, has been cloned in plasmid vectors after cleavage with various restriction enzymes. By a combination of Northern blot hybridization and nucleotide sequence analysis we have characterized most of the P. lividus mitochondrial transcripts and determined the basic gene organization of the mtDNA. The nucleotide sequence of a gene for one NADH dehydrogenase (ND) subunit, ND4L, has also been determined. Our results show the existence of a novel gene order. The 12S and 16S rRNA genes are not contiguous but are separated from each other by ND1 and ND2 genes. The ND4L gene is not adjacent to ND4 but is located between the tRNAArg gene and the gene for subunit II of cytochrome oxidase (CoII). The tRNA genes are reshuffled and contrary to all vertebrate mitochondrial genomes studied so far, there are no intergenic regions between the tRNAPhe and the cytochrome b genes. These characteristics suggest a peculiar mechanism for the regulation of gene expression in this organism and provide information on the evolution of the mitochondrial genetic system in animal cells.