Nucleotide sequence of the mitochondrial genome of<i>Paramecium</i>

Pritchard, A. E.; Seilhamer, Jeffrey J.; Mahalingam, Ravi; Sable, Carol L.; Venuti, Susan E.; Cummings, Donald J.

doi:10.1093/nar/18.1.173

Cited by 146 publications

(103 citation statements)

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“…This is likely due to the fact that the only available sequences of cox-1 in ciliates are those from species of the genera Paramecium and Tetrahymena. To date, only six complete ciliate mtDNA genomes are available: for Tetrahymena thermophila, Tetrahymena pyriformis, Tetrahymena paravorax, Tetrahymena malaccensis, Tetrahymena pigmentosa, and P. aurelia (9,10,46,52).…”

Section: Discussionmentioning

confidence: 99%

High-Level Genetic Diversity but No Population Structure Inferred from Nuclear and Mitochondrial Markers of the Peritrichous CiliateCarchesium polypinumin the Grand River Basin (North America)

Gentekaki

Lynn

2009

Appl Environ Microbiol

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Studies that assess intraspecific genetic variation in ciliates are few and quite recent. Consequently, knowledge of the subject and understanding of the processes that underlie it are limited. We sought to assess the degree of intraspecific genetic variation in Carchesium polypinum (Ciliophora: Peritrichia), a cosmopolitan, freshwater ciliate. We isolated colonies of C. polypinum from locations in the Grand River basin in Southwestern Ontario, Canada. We then used the nuclear markers-ITS1, ITS2, and the hypervariable regions of the large subunit rRNA-and an 819-bp fragment of the mitochondrial cytochrome c oxidase I gene (cox-1) to investigate the intraspecific genetic variation of C. polypinum and the degree of resolution of the above-mentioned markers at the population level. We also sought to determine whether the organism demonstrated any population structure that mapped onto the geography of the region. Our study shows that there is a high degree of genetic diversity at the isolate level, revealed by the mitochondrial markers but not the nuclear markers. Furthermore, our results indicate that C. polypinum is likely not a single morphospecies as previously thought.Studies of intraspecific genetic variation in macroorganisms have provided insights into microevolutionary processes and speciation in these organisms. However, our understanding of the intraspecific genetic diversity of microbial eukaryotes and its temporal and spatial distribution is neither deep nor broad due to the limited number of studies that deal with these topics (2,5,7,31).Many of the studies assessing within-species genetic variation and its distribution have used random amplified polymorphic DNA (RAPD) fingerprinting. Typically, the amount of genetic variation is very low within a species (35,36,56), with some exceptions (20, 57). However, there are several problems arising from the use of RAPDs as the sole source of data, including reproducibility and scoring concerns (54).Sequences of the internal transcribed spacers (ITS), namely, ITS1 and ITS2, of the rRNA region have also been used to study the genetic diversity and population structure of protists (2, 6, 44). In several instances, the ITS sequences of populations of ciliates from across the globe have been nearly identical, indicating very low genetic variation (4, 13, 59, 62). On the other hand, the hypervariable regions of the large subunit (LSU) rRNA have revealed moderate genetic diversity in ciliates at the population level (15, 51).Mitochondrial DNA (mtDNA) has been employed only sparingly in population studies of protists, even though it is routinely used in similar studies of metazoans (3,7,8). Of the mitochondrial genes, the apocytochrome b gene (cob) and the cytochrome c oxidase I (cox-1) gene (cox-1) have been used for population-level analyses of ciliates. Estimation of intraspecific nucleotide diversity of the cob gene from three species of the prostome ciliate Coleps showed only minor differences (5). On the other hand, the cox-1 gene revealed genetic diversity that...

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Section: Discussionmentioning

confidence: 99%

High-Level Genetic Diversity but No Population Structure Inferred from Nuclear and Mitochondrial Markers of the Peritrichous CiliateCarchesium polypinumin the Grand River Basin (North America)

Gentekaki

Lynn

2009

Appl Environ Microbiol

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“…Other organisms that lack the atp6 gene in their mitochondrial genomes and that are likely to have transferred it to the nucleus are the closely related algae C. eugametos (9) and C. elongatum (10), the apicomplexan organisms P. falciparum (41) and Plasmodium reinchenowi (44), and the ciliates Paramecium aurelia (45) and Tetrahymena pyriformis (46). It would be interesting to examine the sequences of ATP6 from more distantly related organisms to determine whether they have reduced physical constraints for import and to determine where reductions in hydrophobicity occur in the protein.…”

Section: Discussionmentioning

confidence: 99%

The Typically Mitochondrial DNA-encoded ATP6 Subunit of the F1F0-ATPase Is Encoded by a Nuclear Gene in Chlamydomonas reinhardtii

Funes¹,

Davidson²,

Claros³

et al. 2002

Journal of Biological Chemistry

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The atp6 gene, encoding the ATP6 subunit of F 1 F 0 -ATP synthase, has thus far been found only as an mtDNA-encoded gene. However, atp6 is absent from mtDNAs of some species, including that of Chlamydomonas reinhardtii. Analysis of C. reinhardtii expressed sequence tags revealed three overlapping sequences that encoded a protein with similarity to ATP6 proteins. PCR and 5-and 3-RACE were used to obtain the complete cDNA and genomic sequences of C. reinhardtii atp6. The atp6 gene exhibited characteristics of a nucleus-encoded gene: Southern hybridization signals consistent with nuclear localization, the presence of introns, and a codon usage and a polyadenylation signal typical of nuclear genes. The corresponding ATP6 protein was confirmed as a subunit of the mitochondrial F 1 F 0 -ATP synthase from C. reinhardtii by N-terminal sequencing. The predicted ATP6 polypeptide has a 107-amino acid cleavable mitochondrial targeting sequence. The mean hydrophobicity of the protein is decreased in those transmembrane regions that are predicted not to participate directly in proton translocation or in intersubunit contacts with the multimeric ring of c subunits. This is the first example of a mitochondrial protein with more than two transmembrane stretches, directly involved in proton translocation, that is nucleus-encoded.

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“…The amino acid numbers on the right refer to individual proteins. Abbreviations and references: kLt, kinetoplast L. tarentolae; cCr, chloroplast Chlamydomonas reinhardtii (26); cEg, chloroplast Euglena gracilis (31); cMp, chloroplast Marchantia polymorpha (34); cCp, cyanelle (chloroplast) Cyanophora paradoxa (23); Ec, E. coli (37); Ml, Micrococcus luteus (33); mPt, mitochondrial P. tetraurelia (38); mZm, mitochondrial Z. mays (15).…”

Section: Vl T L Vtmentioning

confidence: 99%

An intergenic G-rich region in Leishmania tarentolae kinetoplast maxicircle DNA is a pan-edited cryptogene encoding ribosomal protein S12.

Maslov¹,

Sturm²,

Niner³

et al. 1992

Mol. Cell. Biol.

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Six short G-rich intergenic regions in the maxicircle of Leishmania tarentolae are conserved in location and polarity in two other kinetoplastid species. We show here that G-rich region 6 (G6) represents a pan-edited cryptogene which contains at least two domains edited independently in a 3'-to-5' manner connected by short unedited regions. In the completely edited RNA, 117 uridines are added at 49 sites and 32 uridines are deleted at 13 sites, creating a translated 85-amino-acid polypeptide. Similar polypeptides are probably encoded by pan-edited G6 transcripts in two other species. The G6 polypeptide has significant sequence similarity to the family of S12 ribosomal proteins. A minicircle-encoded gRNA overlaps 12 editing sites in G6 mRNA, and chimeric gRNA/mRNA molecules were shown to exist, in agreement with the transesterification model for editing.The mRNA transcripts of several mitochondrial genes in kinetoplastid protozoa are modified by a novel posttranscriptional process known as RNA editing, in which uridine residues are added to and occasionally deleted from coding regions (2, 3, 44, 48, 52). RNA editing, in effect, is a mechanism to decipher the primary transcripts of the six known cryptogenes-cytochrome b, cytochrome oxidase subunits II and III (COII and COIII), NADH dehydrogenase subunit 7 (ND7), and unidentified reading frames 2 (MURF2) and 4 (MURF4)-in such a way that functional translation products can be obtained by the mitochondrial translation system. However, the mitochondrial genomic information content of kinetoplastids is still somewhat limited compared with that found in other eukaryotic cells such as yeast and human cells: no F,F0 ATPase subunit genes and no mitochondrial tRNA genes (16, 40) have been identified in the maxicircle genome. Identification of the MURF4 sequence as subunit 6 of the F, ATPase has been suggested (4), but the alignments with known ATPase subunit 6 sequences are not statistically significant (45).Extensive or pan-editing of the ND7, COIII, and MURF4 maxicircle cryptogenes is limited to Trypanosoma brucei (4,11,22). In Leishmania tarentolae and Crithidia fasciculata (48), the ND7 mRNA is both 5' edited and internally edited, and the MURF4 mRNA is pan-edited only in the 5' portion (4). Originally it seemed that pan-editing was limited to the African trypanosomes. However, on the basis of the distinctive G+A-rich character of the preedited regions of known cryptogenes, Simpson and Shaw (48) hypothesized that six short G-rich maxicircle intergenic regions which were conserved in relative location and polarity, but not in sequence, in L. tarentolae, T. brucei and C. fasciculata actually represented pan-edited cryptogenes encoding additional mitochondrial genetic information. Heterogeneously sized transcripts from these regions had previously been identified in T. brucei (18). * Corresponding author.We show in this report that this hypothesis is correct for G-rich region 6 (G6) in L. tarentolae, and we show that the putative translated polypeptide from the G6 edited m...

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Nucleotide sequence of the mitochondrial genome ofParamecium

Cited by 146 publications

References 59 publications

High-Level Genetic Diversity but No Population Structure Inferred from Nuclear and Mitochondrial Markers of the Peritrichous CiliateCarchesium polypinumin the Grand River Basin (North America)

High-Level Genetic Diversity but No Population Structure Inferred from Nuclear and Mitochondrial Markers of the Peritrichous CiliateCarchesium polypinumin the Grand River Basin (North America)

The Typically Mitochondrial DNA-encoded ATP6 Subunit of the F1F0-ATPase Is Encoded by a Nuclear Gene in Chlamydomonas reinhardtii

An intergenic G-rich region in Leishmania tarentolae kinetoplast maxicircle DNA is a pan-edited cryptogene encoding ribosomal protein S12.

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