Evaluating the utility of cox1 for cetacean species identification

The mitochondrial cytochrome c oxidase I (cox1) gene has been promoted as a universal reference gene, or barcode, to identify organisms to the species level. We evaluated whether cox1 would be appropriate to diagnose cetacean species. The 5′ end of cox1 (686 base pairs, bp) was sequenced for 46 of 86 recognized species of cetaceans. In addition, we included 105 sequences from GenBank, increasing our taxonomic coverage to 61 species. Particular focus was placed on sampling two subfamilies that contain closely related taxa: the Delphininae and the Globicephalinae. Species‐specific sequences were observed for all but three taxa (Delphinus delphis, D. capensis, and Stenella coeruleoalba). Although correct assignment was seen for most species, significant overlap between intra‐ and interspecific variation makes cox1 an imperfect barcode for cetaceans. The efficacy of cox1 was compared to the 5′ end of the cytochrome b (cytb) gene, a mitochondrial region routinely used for cetacean species identification. Although cytb performed better than cox1 for some species, this marker could not differentiate other closely related taxa (Eubalaena spp.). Species identification for taxa not reliably identified using cox1 or cytb might be best addressed through use of multiple mitochondrial DNA fragments or other newly developed markers.     

Cloning and DNA-binding properties of ethylene response factor,LeERF1 and LeERF2, in tomato

Two new genes, LeERF1 andLeERF2, were isolated from a tomato (Lycopersicon esculentum cv. Lichun) cDNA library. Phylogenetic analysis indicated that they encoded Ethylene Responsive Element Binding Proteins (EREBPs), characterized by a conserved ERF (ethylene response factor) domain of specific binding plant cis-acting elements GCC box. Both LeERF1 and LeERF2 proteins were obtained via prokaryotic expression and purification. Electrophoretic mobility shift assay showed that LeERF1 and LeERF2 protein could bind to the promoter of the NP24 gene coding for pathogenesis-related protein osmotin precursor but not the mutant promoter where its GCC box was deleted. Polyclonal antibodies of LeERF1 and LeERF2 blocked their binding in vitro.Revisions requested 4 January 2005; Revisions received 28 January 2005     

Footprints of unconventional mitochondrial inheritance in bivalve phylogeny: Signatures of positive selection on clades with doubly uniparental inheritance

The doubly uniparental inheritance (DUI) of some bivalve mollusks is the major exception to the common maternal inheritance of mitochondria in animals. DUI involves two mitochondrial lineages with paternal and maternal transmission routes, and it appears as a complex phenomenon requiring both nuclear and mitochondrial adaptations. DUI distribution seems to be scattered among the Bivalvia, and there are several clues for its multiple origins. In this paper, we investigate whether the incipient DUI systems had left possible selective signatures on mitochondrial genomes. Alongside the outstanding divergence of amino acid sequences, we confirmed strong purifying selection to act on mitochondrial genes. However, we found evidence that distinct episodes of intense directional pressure are associated with the origins of different DUI systems: We interpret these signals as footprints of the coevolution with the nuclear genome that ought to take place at the base of a DUI clade. Six genes (atp6, cox1, cox2, cox3, nad4L, and nad6) seem to be more commonly linked to the appearance of DUI. We also identified few putative DUI‐specific mutations, thus extending support to the hypothesis of multiple independent origins of this complex phenomenon.     

A survey of Polytomella (Chlorophyceae,Chlorophyta) strains in public culture collections

Polytomella is a genus of colorless green algae in the Reinhardtinia clade of the Chlamydomonadales, which has proven useful for a broad range of studies particularly those exploring the evolutionary loss of photosynthesis and mitochondrial genomics/biochemistry. Although 13 Polytomella strain accessions are currently available from public culture collections, the taxonomic status and redundancy of many of these strains is not clear because of possible mix‐ups, deficient historical records, and incomplete molecular data. This study therefore considers previously available and/or new cox1 and mitochondrial DNA telomere sequences from all 13 Polytomella strain accessions. Among four of these, namely P. parva SAG 63‐3, P. piriformis SAG 63‐10, P. capuana SAG 63‐5, and P. magna SAG 63‐9, cox1 and mitochondrial telomere regions are both highly divergent between strains. All of the remaining nine Polytomella strain accessions have cox1 sequences that are identical to that of P. parva SAG 63‐3 and although five of these have a mitochondrial telomere haplotype that is identical to that of P. parva SAG 63‐3, the remaining four have one of three different haplotypes. Among the 10 strains with identical cox1 sequences, we suggest that three of the telomere haplotypes are associated with distinct geographical isolates of Polytomella and the fourth evolved from one of these isolates during 50 years of active culture.     

Species‐specific mitochondrial gene rearrangements in biting midges and vector species identification

Abstract Partial mitochondrial gene sequences of 16 Culicoides species were determined to elucidate phylogenetic relations among species and to develop a molecular identification method for important virus vector species. In addition, the analysis found mitochondrial gene rearrangement in several species. Sequences of the mitochondrial genome region, cox1–trnL2–cox2 (1940–3785 bp) of 16 Culicoides and additional sequences were determined in some species, including whole mitochondrial genome sequences of Culicoides arakawae. Nine species showed common organization in this region, with three genes cox1–trnL2–cox2 and a small or no intergenic region (0–30 bp) between them. The other seven species showed translocation of tRNA and protein‐coding genes and/or insertion of AT‐rich non‐coding sequences (65–1846 bp) between the genes. The varied gene rearrangements among species within a genus is very rare for mitochondrial genome organization. Phylogenetic analyses based on the sequences of cox1+cox2 suggest a few clades among Japanese Culicoides species. No relationships between phylogenetic closeness and mitochondrial gene rearrangements were observed. Sequence data were used to establish a polymerase chain reaction tool to distinguish three important vector species from other Culicoides species, for which classification during larval stages is not advanced and identification is difficult.     

The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization

We present an overview of the gene content and organization of the mitochondrial genome of Dictyostelium discoideum. The mitochondria genome consists of 55,564 bp with an A + T content of 72.6%. The identified genes include those for two ribosomal RNAs (rnl and rns), 18 tRNAs, ten subunits of the NADH dehydrogenase complex (nad1, 2, 3, 4, 4L, 5, 6, 7, 9 and 11), apocytochrome b (cytb), three subunits of the cytochrome oxidase (cox1/2 and 3), four subunits of the ATP synthase complex (atp1, 6, 8 and 9), 15 ribosomal proteins, and five other ORFs, excluding intronic ORFs. Notable features of D. discoideum mtDNA include the following. (1) All genes are encoded on the same strand of the DNA and a universal genetic code is used. (2) The cox1 gene has no termination codon and is fused to the downstream cox2 gene. The 13 genes for ribosomal proteins and four ORF genes form a cluster 15.4 kb long with several gene overlaps. (3) The number of tRNAs encoded in the genome is not sufficient to support the synthesis of mitochondrial protein. (4) In total, five group I introns reside in rnl and cox1/2, and three of those in cox1/2 contain four free-standing ORFs. We compare the genome to other sequenced mitochondrial genomes, particularly that of Acanthamoeba castellanii. Received: 5 July 1999 / Accepted: 17 January 2000     

A Complex Organization of the Gene Encoding Cytochrome Oxidase Subunit 1 in the Mitochondrial Genome of the Dinoflagellate, Crypthecodinium cohnii: Homologous Recombination Generates Two Different cox1 Open Reading Frames

In the course of investigating mitochondrial genome organization in Crypthecodinium cohnii, a non-photosynthetic dinoflagellate, we identified four EcoRI fragments that hybridize to a probe specific for cox1, the gene that encodes subunit 1 of cytochrome oxidase. Cloning and sequence characterization of the four fragments (5.7, 5.1, 4.1, 3.5 kilobase pairs) revealed that cox1 exists in four distinct but related contexts in C. cohnii mtDNA, with a central repeat unit flanked by one of two possible upstream (flanking domain 1 or 2) and downstream (flanking domain 3 or 4) regions. The majority of the cox1 gene is located within the central repeat; however, the C-terminal portion of the open reading frame extends into flanking domains 3 and 4, thereby creating two distinct cox1 coding sequences. The 3′-terminal region of one of the cox1 reading frames can assume an elaborate secondary structure, which potentially could act to stabilize the mature mRNA against nucleolytic degradation. In addition, a high density of small inverted repeats (15–22 base pairs) has been identified at the 5′-end of cox1, further suggesting that hairpin structures could be important for gene regulation. The organization of cox1 in C. cohnii mtDNA appears to reflect homologous recombination events within the central repeat between different cox1 sequence contexts. Such recombining repeats are a characteristic feature of plant (angiosperm) mtDNA, but they have not previously been described in the mitochondrial genomes of protists. Received: 21 December 2000 / Accepted: 30 January 2001     

The mitochondrial genome of fission yeast: inability of all introns to splice autocatalytically, and construction and characterization of an intronless genome

Summary In this paper we report the inability of four group I introns in the gene encoding subunit I of cytochrome c oxidase (cox1) and the group II intron in the apocytochrome b gene (cob) to splice autocatalytically. Furthermore we present the characterization of the first cox1 intron in the mutator strain ana ^r -14 and the construction and characterization of strains with intronless mitochondrial genomes. We provide evidence that removal of introns at the DNA level (termed DNA splicing) is dependent on an active RNA maturase. Finally we demonstrate that the absence of introns does not abolish homologous mitochondrial recombination.Abbreviations cox1, cox2, cox3 genes encoding subunits 1, 2 and 3 of cytochrome - c oxidase - cob gene encoding apocytochrome b - cox1I1, cox1I2a, cox1I2b, cox1I3 introns in cox1 - cox1Ix ^+/– indicates the presence or absence of the intron either in the native gene or after intron DNA excision - cox1Ix is a deletion in the intron leading to respiratory deficiency     

Effects of dietary lipid levels on mitochondrial gene expression in low and high‐feed efficient families of rainbow trout Oncorhynchus mykiss

A 2 × 3 factorial study was conducted to evaluate the effects of dietary lipid level on mitochondrial gene expression in mixed sex rainbow trout Oncorhynchus mykiss. Practical diets with a fixed crude protein content of 42%, formulated to contain 10% (42/10), 20% (42/20) and 30% (42/30) dietary lipid, were fed to triplicate groups of either low‐feed efficient (F129; mean ± s.d. = 105·67 ± 3·04 g initial average mass) or high‐feed efficient (F134; mean ± s.d. = 97·86 ± 4·02 g) families of fish, to apparent satiety, twice per day, for 108 days. At the end of the experiment, diets 42/20 and 42/30 led to similar fish condition factors, which were higher than that observed with diet 42/10 (P < 0·05). F134 fish fed diet 42/10 showed the highest hepato‐somatic index, while there was no significant difference among all the other treatments (P < 0·05). When the group of F134 fish fed diet 42/10 was used as the calibrator for gene expression analysis, the five genes selected for their involvement in lipid metabolism (complex I‐nd1, complex III‐cytb, complex IV‐cox1, complex IV‐cox2 and complex V‐atp6) were up‐regulated in the muscle and down‐regulated in both the liver and the intestine. There was a significant family × diet interaction regarding nd1, cox2 and atp6 in the liver; nd1, cytb, cox1, cox2 and atp6 in the intestine, and nd1, cytb, cox1, cox2 and atp6 in the muscle (P < 0·05). The overall results of this study constitute basic information for the understanding of molecular mechanisms of lipid metabolism at the mitochondrial level in fishes.     

A RAD52‐like single‐stranded DNA binding protein affects mitochondrial DNA repair by recombination

The plant mitochondrial DNA‐binding protein ODB1 was identified from a mitochondrial extract after DNA‐affinity purification. ODB1 (organellar DNA‐binding protein 1) co‐purified with WHY2, a mitochondrial member of the WHIRLY family of plant‐specific proteins involved in the repair of organellar DNA. The Arabidopsis thaliana ODB1 gene is identical to RAD52‐1, which encodes a protein functioning in homologous recombination in the nucleus but additionally localizing to mitochondria. We confirmed the mitochondrial localization of ODB1 by in vitro and in vivo import assays, as well as by immunodetection on Arabidopsis subcellular fractions. In mitochondria, WHY2 and ODB1 were found in large nucleo‐protein complexes. Both proteins co‐immunoprecipitated in a DNA‐dependent manner. In vitro assays confirmed DNA binding by ODB1 and showed that the protein has higher affinity for single‐stranded than for double‐stranded DNA. ODB1 showed no sequence specificity in vitro. In vivo, DNA co‐immunoprecipitation indicated that ODB1 binds sequences throughout the mitochondrial genome. ODB1 promoted annealing of complementary DNA sequences, suggesting a RAD52‐like function as a recombination mediator. Arabidopsis odb1 mutants were morphologically indistinguishable from the wild‐type, but following DNA damage by genotoxic stress, they showed reduced mitochondrial homologous recombination activity. Under the same conditions, the odb1 mutants showed an increase in illegitimate repair bypasses generated by microhomology‐mediated recombination. These observations identify ODB1 as a further component of homologous recombination‐dependent DNA repair in plant mitochondria.     

UTILITY OF THE MITOCHONDRIAL nad4L GENE FOR ALGAL AND PROTISTAN PHYLOGENETIC ANALYSIS1

Mitochondrial gene sequences, in contrast to their plastid counterparts, have been rarely exploited for use in determining algal phylogenetic relationships. Their utilization would prove advantageous particularly for the assessment of evolutionary relationships among protistan lineages that include photo synthetic species and their colorless heterotrophic dependents that contain only a reduced plastid genome as well as ancestral nonphotosynthetic relatives. Recent studies that have examined mitochondrial protein (coxl, cox2, cob, and nad5) rather than ribosomal RNA genes confirm that these algal sequences are sufficiently conserved to be used routinely in algal systematics. In this investigation, we sequenced the mitochondrial nad4L gene, encoding a small (ca. 99-amino acid) polypeptide subunit of the NADH dehydrogenase complex, from two chromophytic algae and an oomycete to determine its suitability for use in determining algal and protistan evolutionary relationships. Our analysis demonstrated that nad4L could clearly resolve these three organisms as a distinct clade, the stramenopiles, to the exclusion of terrestrial plants/chlorophytes and eufungi. However, the position of deeply rooted species within the stramenopiles proved tenuous and would best be examined in conjunction with the analysis of longer mitochondrial protein gene sequences.     

膜蛋白ATAD3A在线粒体质量控制中的作用

线粒体质量控制对于线粒体网络的稳态和线粒体功能的正常发挥具有重要意义。三磷酸腺苷酶家族蛋白3A(ATAD3A)是同时参与调节线粒体结构功能、线粒体动力学和线粒体自噬等重要生物学过程的线粒体膜蛋白之一。近期研究表明,ATAD3A既可与Mic60/Mitofilin和线粒体转录因子A (TFAM)等因子相互作用以维持线粒体嵴的形态和氧化磷酸化功能,又能与发动蛋白相关蛋白1 (Drp1)结合而正性/负性调节线粒体分裂,还可作为线粒体外膜转位酶（TOM）复合物和线粒体内膜转位酶（TIM）复合物之间的桥接因子而介导PTEN诱导激酶（PINK1）输入线粒体进行加工,显示出促自噬或抗自噬活性。本文对ATAD3A在调控线粒体质量控制中的作用及其机制进行了综述。     

Characterization of the complete mitochondrial genome of Cryptotermes domesticus (Blattodea: Kalotermitidae): Genome description and phylogenetic implications

The complete mitochondrial genome of Cryptotermes domesticus (Haviland) was sequenced and annotated to study its characteristics and the phylogenetic relationship of C. domesticus to other termite species. The mitogenome of C. domesticus is a circular, close, and double-stranded molecule with a length of 15,655 bp. The sequenced mitogenome contains 37 typical genes, which are highly conserved in gene size, organization, and codon usage. Transfer RNA genes (tRNAs) also have typical secondary structures. All of the 13 protein-coding genes (PCGs) start with an ATN codon, except for nad4, which starts with GTG and terminates with the terminal codon TAA and TAG or the incomplete form T-- (cox2 and nad5). Most tRNAs have a typical cloverleaf structure, except for trnS1, in which this form is replaced by a simple loop and lacks the dihydrouridine (DHU) arm. The nucleotide diversity (Pi) and nonsynonymous (Ka)/synonymous (Ks) mutation rate ratios indicate that nad1, cox1, and cox3 are the most conserved genes, and that cox1 has the lowest rate of evolution. In addition, an 89 bp repeated sequence was found in the A + T-rich region. Phylogenetic analysis was performed using Bayesian inference (BI) and maximum likelihood (ML) methods based on 13 PCGs, and the monophyly of Kalotermitidae was supported.     

Diversity of sponge mitochondrial introns revealed by <Emphasis Type="Italic">cox 1</Emphasis>sequences of Tetillidae

Background  

Animal mitochondrial introns are rare. In sponges and cnidarians they have been found in the cox 1 gene of some spirophorid and homosclerophorid sponges, as well as in the cox 1 and nad 5 genes of some Hexacorallia. Their sporadic distribution has raised a debate as to whether these mobile elements have been vertically or horizontally transmitted among their hosts. The first sponge found to possess a mitochondrial intron was a spirophorid sponge from the Tetillidae family. To better understand the mode of transmission of mitochondrial introns in sponges, we studied cox 1 intron distribution among representatives of this family.