Putative chicken "muscle-specific 7 S RNA" is related to the mitochondrial ATPase 6 gene

The necessity of mitochondrial genome DNA for normal development of Dictyostelium cells

Most unexpectedly, there is now increasing evidence that mitochondria have novel and crucial functions in the regulatory machinery of the growth/differentiation transition, cell-type determination, cellular movement and pattern formation. Here we created rho delta cells with a reduced amount (about 1/4) of mitochondrial DNA (mtDNA) from Dictyostelium discoideum Ax-2 cells, by exposing Ax-2 cells to ca. 30 microg/ml of ethidium bromide (EtBr) in axenic growth medium. Importantly, the rho delta cells exhibited a series of fascinating behaviors: when they were starved, they showed a marked delay of differentiation and stopped their development at the slug stage, thus failing to construct fruiting bodies. Moreover, cell patterning and cell-type proportioning were found to be greatly modified in slugs (referred to as rho delta slugs) derived from rho delta cells. That is, prestalk differentiation was significantly enhanced in rho delta slugs, while prespore differentiation was markedly inhibited. In addition, the clear anterior prestalk/posterior prespore pattern was considerably disturbed in rho delta slugs, presumably because of incomplete sorting between the two types of differentiated cells. After the assay of phototaxis, rho delta slugs also exhibited highly disordered movement towards the light source. Taken together, these results suggest that mtDNA might have important multiple functions in a variety of cellular processes during Dictyostelium development.

Regulation of growth and differentiation in Dictyostelium

In general, growth and differentiation are mutually exclusive, but they are cooperatively regulated during the course of development. Thus, the process of a cell's transition from growth to differentiation is of general importance not only for the development of organisms but also for the initiation of malignant transformation, in which this process is reversed. The cellular slime mold Dictyostelium, a wonderful model organism, grows and multiplies as long as nutrients are supplied, and its differentiation is triggered by starvation. A strict checkpoint (growth/differentiation transition or GDT point), from which cells start differentiating in response to starvation, has been specified in the cell cycle of D. discoideum Ax-2 cells. Accordingly, integration of GDT point-specific events with starvation-induced events is needed to understand the mechanism regulating GDTs. A variety of intercellular and intracellular signals are involved positively or negatively in the initiation of differentiation, making a series of cross-talks. As was expected from the presence of GDT points, the cell's positioning in cell masses and subsequent cell-type choices occur depending on the cell's phase in the cell cycle at the onset of starvation. Since novel and somewhat unexpected multiple functions of mitochondria in cell movement, differentiation, and pattern formation have been well realized in Dictyostelium cells, they are reviewed in this article.

Cloning and characterization of cDNAs encoding chicken mitogen-activated protein kinase kinase type 2, MEK2: downregulation of MEK2 in response to inhibition of mitochondrial DNA expression

The present work was initiated with the aim of identifying nuclear genes whose expression is sensitive to the mitochondrial DNA (mtDNA) status of transformed chicken DU24 cells. We cloned and sequenced cDNAs for the mitogen-activated protein kinase kinase type 2, MEK2, a protein involved in the mitogenic growth factor signal transduction pathway in vertebrates. Sequence comparisons between the chicken protein and its mammalian counterparts indicated that MEK2 proteins are highly conserved among vertebrates. Southern blot analysis of endonuclease-digested genomic DNA from primary chick embryo fibroblasts (CEF) suggested that MEK2 is a single-copy gene in this vertebrate species. The steady-state level of MEK2 transcripts is decreased in DUS3 mtDNA-less (rho0) cells developed by long-term exposure of DU24 rho+ cells to ethidium bromide (EtdBr). Run-on in vitro transcription assays and mRNA stability studies indicated that the decrease in MEK2 mRNA content is associated with post-transcriptional regulation. In parental DU24 cells, MEK2 mRNA content decreased after inhibition of mtDNA transcription by EtdBr and inhibition of translation on mitoribosomes by chloramphenicol (CAM). Cytoplasmic hybrids (cybrids) constructed by fusion of chicken rho0 cells with enucleated parental cells and CEF recovered a basal level of MEK2 expression. The MEK2 protein content is decreased in DUS3 rho0 cells and in parental DU24 rho+ cells treated with EtdBr and CAM for 6 days, while that of MEK1, a closely related kinase, remained unchanged. On the basis of these observations, we propose that mitochondria participate in the mitogenic signal transduction pathway in chicken cells through regulation of MEK2 expression.

Up-regulation of nuclear genes in response to inhibition of mitochondrial DNA expression in chicken cells

Vertebrate cells depleted of (rho0) mitochondrial DNA (mtDNA) exhibited phenotypic traits that differed from the parental (rho+) cells. To isolate genes whose expression is associated with mtDNA depletion, we constructed cDNA libraries from mRNAs isolated from chicken rho+ cells transformed by the MC29 (v-myc-containing) retrovirus and from rho0 cells developed by long-term exposure of the rho+ cells to ethidium bromide (EtdBr). Through subtractive hybridization procedures, three genes, elongation factor 1 alpha (EF- 1 alpha), beta-actin and v-myc were identified and found to be up-regulated in rho0 cells. In addition, Northern analysis demonstrated that the mRNA content for GAPDH was also elevated in rho0 cells. Run-on transcription assays and mRNA stability studies in the presence of actinomycin D indicated that elevated expression of these four genes depends, at least in part, upon increased rate of transcription. Other regulatory mechanisms contribute to the elevated expression of the transcripts in rho0 cells, as suggested by cycloheximide enhancement of the accumulation of the mRNAs for EF-1 alpha and beta-actin in rho0 cells, but not in parental rho+ cells. Moreover, inhibition of mtDNA replication and transcription by EtdBr and inhibition of translation on mitoribosomes by chloramphenicol also increased the expression of the four genes in parental rho+ cells, thus mimicking the situation in rho0 cells. These data suggest that information encoded within mtDNA participates in the regulation of nuclear genes in chicken cells.

Cloning and characterization of a cDNA encoding elongation factor 1 alpha from chicken cells devoid of mitochondrial DNA

Using a subtractive hybridization procedure, we isolated a cDNA clone encoding elongation factor 1 alpha (EF-1 alpha) from chicken cells devoid of mitochondrial (mt) DNA (rho0). The sequence encodes 1691 nucleotide (nt) residues and contains an open reading frame of 463 codons. Compared with the sequences from human, mouse and Xenopus laevis, the highest degree of sequence identity is detected in the 3' untranslated (> 90%) and coding (> 85%) regions. The gene evolved mainly by transitions occurring at the third codon position. Most transitions are silent and amino acid (aa) sequence identities are greater than 95%. Comparison of the protein domains interacting with cellular components (GTP/GDP, tRNAs and beta-actin) reveals that they are highly conserved in species belonging to the four traditional eukaryotic kingdoms. The expression of the EF-1 alpha transcript is elevated in chicken rho0 cells. A single RNA band at 1800 nt is observed in both parental and rho0 cells. Southern blot analysis of restricted DNA from chick embryo fibroblasts (CEF) suggests that only one gene encoding EF-1 alpha exists in the chicken genome.

The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome

The complete sequence of the carp mitochondrial genome of 16,575 base pairs has been determined. The carp mitochondrial genome encodes the same set of genes (13 proteins, 2 rRNAs, and 22 tRNAs) as do other vertebrate mitochondrial DNAs. Comparison of this teleostean mitochondrial genome with those of other vertebrates reveals a similar gene order and compact genomic organization. The codon usage of proteins of carp mitochondrial genome is similar to that of other vertebrates. The phylogenetic relationship for mitochondrial protein genes is more apparent than that for the mitochondrial tRNA and rRNA genes.

The two ATPase 6 mRNAs of Leishmania tarentolae differ at their 3' ends

We have determined the complete nucleotide sequence of ATPase 6 mRNA from Leishmania tarentolae. RNA editing occurs only in the 5' one-third of the mRNA and is the most extensive observed to date in this species. We have identified a potential gRNA sequence, encoded in a minicircle, for a portion of the edited sequence. The predicted amino acid sequence is about 85% homologous to that predicted from the more extensively edited Trypanosoma brucei ATPase 6 mRNA. The edited L. tarentolae mRNA exists as two distinct size classes which differ in the size of their 3' ends. Although variation in the length of the 3' untranslated region cannot be excluded, the size difference is probably to be due to variation in the length of the poly(A) tail.

Heart development in normal and cardiac-lethal mutant axolotls: a model for the control of vertebrate cardiogenesis

The mechanisms which regulate myocardial differentiation are poorly understood. The cardiac-lethal (c) mutant of Ambystoma mexicanum, in which the heart never begins to beat, provides a valuable model system for studying this process. Using an in vitro assay, we examine the nature of the defect in c/c embryos and find (contrary to previous reports) that the inductive endoderm is not affected by the mutation. Rather, the pre-cardiac mesoderm is directly affected by the c gene and is incapable of responding to normal inductive influences. Furthermore, we find that mutant mesoderm can complete its differentiation into functional cardiomyocytes when co-cultured with wild-type heart mesoderm. With this evidence, we propose a model for the regulation of heart differentiation based on the migration of the heart mesoderm over a gradient of inducer, and the subsequent establishment of a two-component reaction-diffusion system within the mesoderm itself. This model has the potential to explain several poorly understood aspects of cardiogenesis, including the gradual nature of heart induction, the restriction of the heart field, and possibly the early morphogenesis of the heart tube.

Nucleotide sequence and evolution of coding and noncoding regions of a quail mitochondrial genome

Segments of the Japanese quail mitochondrial genome encompassing many tRNA and protein genes, the small and part of the large rRNA genes, and the control region have been cloned and sequenced. Analysis of the relative position of these genes confirmed that the tRNA(Glu) and ND6 genes in galliform mitochondrial DNA are located immediately adjacent to the control region of the molecule instead of between the cytochrome b and ND5 genes as in other vertebrates. Japanese quail and chicken display another distinctive characteristic, that is, they both lack an equivalent to the light-strand replication origin found between the tRNA(Cys) and tRNA(Asn) genes in all vertebrate mitochondrial genomes sequenced thus far. Comparison of the protein-encoding genes revealed that a great proportion of the substitutions are silent and involve mainly transitions. This bias toward transitions also occurs in the tRNA and rRNA genes but is not observed in the control region where transversions account for many of the substitutions. Sequence alignment indicated that the two avian control regions evolve mainly through base substitutions but are also characterized by the occurrence of a 57-bp deletion/addition event at their 5' end. The overall sequence divergence between the two gallinaceous birds suggests that avian mitochondrial genomes evolve at a similar rate to other vertebrate mitochondrial DNAs.

Mutagenesis of the a subunit of the F1F0-ATP synthase from Escherichia coli in the region of Asn-192

Site-directed cassette mutagenesis was used to generate a series of amino acid substitutions in the a subunit of the Escherichia coli F1F0-ATP synthase. The following substitutions for Asn-192 were analyzed and shown to inhibit partially the ATP-dependent proton translocation without disrupting F1-F0 interactions: Leu, Val, Pro, Ser, Thr, and Arg. A group of multiple substitutions at residues Gln-181, Asn-184, and His-185 had no significant effect on ATP synthase function, as judged by growth yields, or by assays of ATP-dependent proton translocation, indicating that this region of the a subunit is not involved in function. Three double mutants were constructed in order to assess the independence of residues Asn-192, Glu-196, and Asn-214. Results of proton translocation assays of membranes from cells containing these double mutations are consistent with the interpretation that each of these residues is involved with proton movement, and that residues Asn-192 and Glu-196 may be coupled. Finally, the relationship between the mechanism of proton translocation by the E. coli ATP synthase and the chloroplast enzyme was probed by constructing variants of the E. coli a subunit containing several features of homologous chloroplast proteins. It was determined that these chloroplast features, in the region of Glu-196 of the E. coli a subunit,, were detrimental to ATP synthase function.

Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates

The 16,775 base-pair mitochondrial genome of the white Leghorn chicken has been cloned and sequenced. The avian genome encodes the same set of genes (13 proteins, 2 rRNAs and 22 tRNAs) as do other vertebrate mitochondrial DNAs and is organized in a very similar economical fashion. There are very few intergenic nucleotides and several instances of overlaps between protein or tRNA genes. The protein genes are highly similar to their mammalian and amphibian counterparts and are translated according to the same variant genetic code. Despite these highly conserved features, the chicken mitochondrial genome displays two distinctive characteristics. First, it exhibits a novel gene order, the contiguous tRNA(Glu) and ND6 genes are located immediately adjacent to the displacement loop region of the molecule, just ahead of the contiguous tRNA(Pro), tRNA(Thr) and cytochrome b genes, which border the displacement loop region in other vertebrate mitochondrial genomes. This unusual gene order is conserved among the galliform birds. Second, a light-strand replication origin, equivalent to the conserved sequence found between the tRNA(Cys) and tRNA(Asn) genes in all vertebrate mitochondrial genomes sequenced thus far, is absent in the chicken genome. These observations indicate that galliform mitochondrial genomes departed from their mammalian and amphibian counterparts during the course of evolution of vertebrate species. These unexpected characteristics represent useful markers for investigating phylogenetic relationships at a higher taxonomic level.