Structural and content diversity of mitochondrial genome in beet: a comparative genomic analysis.

Despite their monophyletic origin, mitochondrial (mt) genomes of plants and animals have developed contrasted evolutionary paths over time. Animal mt genomes are generally small, compact, and exhibit high mutation rates, whereas plant mt genomes exhibit low mutation rates, little compactness, larger sizes, and highly rearranged structures. We present the (nearly) whole sequences of five new mt genomes in the Beta genus: four from Beta vulgaris and one from B. macrocarpa, a sister species belonging to the same Beta section. We pooled our results with two previously sequenced genomes of B. vulgaris and studied genome diversity at the species level with an emphasis on cytoplasmic male-sterilizing (CMS) genomes. We showed that, contrary to what was previously assumed, all three CMS genomes belong to a single sterile lineage. In addition, the CMSs seem to have undergone an acceleration of the rates of substitution and rearrangement. This study suggests that male sterility emergence might have been favored by faster rates of evolution, unless CMS itself caused faster evolution.

The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution.

Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is a representative of the group of lactic acid-producing bacteria, mainly known for its worldwide application in yogurt production. The genome sequence of this bacterium has been determined and shows the signs of ongoing specialization, with a substantial number of pseudogenes and incomplete metabolic pathways and relatively few regulatory functions. Several unique features of the L. bulgaricus genome support the hypothesis that the genome is in a phase of rapid evolution. (i) Exceptionally high numbers of rRNA and tRNA genes with regard to genome size may indicate that the L. bulgaricus genome has known a recent phase of important size reduction, in agreement with the observed high frequency of gene inactivation and elimination; (ii) a much higher GC content at codon position 3 than expected on the basis of the overall GC content suggests that the composition of the genome is evolving toward a higher GC content; and (iii) the presence of a 47.5-kbp inverted repeat in the replication termination region, an extremely rare feature in bacterial genomes, may be interpreted as a transient stage in genome evolution. The results indicate the adaptation of L. bulgaricus from a plant-associated habitat to the stable protein and lactose-rich milk environment through the loss of superfluous functions and protocooperation with Streptococcus thermophilus.

Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi.

Microsporidia are obligate intracellular parasites infesting many animal groups. Lacking mitochondria and peroxysomes, these unicellular eukaryotes were first considered a deeply branching protist lineage that diverged before the endosymbiotic event that led to mitochondria. The discovery of a gene for a mitochondrial-type chaperone combined with molecular phylogenetic data later implied that microsporidia are atypical fungi that lost mitochondria during evolution. Here we report the DNA sequences of the 11 chromosomes of the approximately 2.9-megabase (Mb) genome of Encephalitozoon cuniculi (1,997 potential protein-coding genes). Genome compaction is reflected by reduced intergenic spacers and by the shortness of most putative proteins relative to their eukaryote orthologues. The strong host dependence is illustrated by the lack of genes for some biosynthetic pathways and for the tricarboxylic acid cycle. Phylogenetic analysis lends substantial credit to the fungal affiliation of microsporidia. Because the E. cuniculi genome contains genes related to some mitochondrial functions (for example, Fe-S cluster assembly), we hypothesize that microsporidia have retained a mitochondrion-derived organelle.

Mechanisms of evolution in Rickettsia conorii and R. prowazekii.

Rickettsia conorii is an obligate intracellular bacterium that causes Mediterranean spotted fever in humans. We determined the 1,268,755-nucleotide complete genome sequence of R. conorii, containing 1374 open reading frames. This genome exhibits 804 of the 834 genes of the previously determined R. prowazekii genome plus 552 supplementary open reading frames and a 10-fold increase in the number of repetitive elements. Despite these differences, the two genomes exhibit a nearly perfect colinearity that allowed the clear identification of different stages of gene alterations with gene remnants and 37 genes split in 105 fragments, of which 59 are transcribed. A 38-kilobase sequence inversion was dated shortly after the divergence of the genus.

The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis.

Mycoplasma pulmonis is a wall-less eubacterium belonging to the Mollicutes (trivial name, mycoplasmas) and responsible for murine respiratory diseases. The genome of strain UAB CTIP is composed of a single circular 963 879 bp chromosome with a G + C content of 26.6 mol%, i.e. the lowest reported among bacteria, Ureaplasma urealyticum apart. This genome contains 782 putative coding sequences (CDSs) covering 91.4% of its length and a function could be assigned to 486 CDSs whilst 92 matched the gene sequences of hypothetical proteins, leaving 204 CDSs without significant database match. The genome contains a single set of rRNA genes and only 29 tRNAs genes. The replication origin oriC was localized by sequence analysis and by using the G + C skew method. Sequence polymorphisms within stretches of repeated nucleotides generate phase-variable protein antigens whilst a recombinase gene is likely to catalyse the site-specific DNA inversions in major M.pulmonis surface antigens. Furthermore, a hemolysin, secreted nucleases and a glyco-protease are predicted virulence factors. Surprisingly, several of the genes previously reported to be essential for a self-replicating minimal cell are missing in the M.pulmonis genome although this one is larger than the other mycoplasma genomes fully sequenced until now.

Genome evolution at the genus level: comparison of three complete genomes of hyperthermophilic archaea.

We have compared three complete genomes of closely related hyperthermophilic species of Archaea belonging to the Pyrococcus genus: Pyrococcus abyssi, Pyrococcus horikoshii, and Pyrococcus furiosus. At the genomic level, the comparison reveals a differential conservation among four regions of the Pyrococcus chromosomes correlated with the location of genetic elements mediating DNA reorganization. This discloses the relative contribution of the major mechanisms that promote genomic plasticity in these Archaea, namely rearrangements linked to the replication terminus, insertion sequence-mediated recombinations, and DNA integration within tRNA genes. The combination of these mechanisms leads to a high level of genomic plasticity in these hyperthermophilic Archaea, at least comparable to the plasticity observed between closely related bacteria. At the proteomic level, the comparison of the three Pyrococcus species sheds light on specific selection pressures acting both on their coding capacities and evolutionary rates. Indeed, thanks to two independent methods, the "reciprocal best hits" approach and a new distance ratio analysis, we detect the false orthology relationships within the Pyrococcus lineage. This reveals a high amount of differential gains and losses of genes since the divergence of the three closely related species. The resulting polymorphism is probably linked to an adaptation of these free-living organisms to differential environmental constraints. As a corollary, we delineate the set of orthologous genes shared by the three species, that is, the genes that may characterize the Pyrococcus genus. In this conserved core, the amino acid substitution rate is equal between P. abyssi and P. horikoshii for most of their shared proteins, even for fast-evolving ones. In contrast, strong discrepancies exist among the substitution rates observed in P. furiosus relative to the two other species, which is in disagreement with the molecular clock hypothesis.

Sequence and analysis of chromosome I of the amitochondriate intracellular parasite Encephalitozoon cuniculi (Microspora).

A DNA sequencing program was applied to the small (<3 Mb) genome of the microsporidian Encephalitozoon cuniculi, an amitochondriate eukaryotic parasite of mammals, and the sequence of the smallest chromosome was determined. The approximately 224-kb E. cuniculi chromosome I exhibits a dyad symmetry characterized by two identical 37-kb subtelomeric regions which are divergently oriented and extend just downstream of the inverted copies of an 8-kb duplicated cluster of six genes. Each subtelomeric region comprises a single 16S-23S rDNA transcription unit, flanked by various tandemly repeated sequences, and ends with approximately 1 kb of heterogeneous telomeric repeats. The central (or core) region of the chromosome harbors a highly compact arrangement of 132 potential protein-coding genes plus two tRNA genes (one gene per 1.14 kb). Most genes occur as single copies with no identified introns. Of these putative genes, only 53 could be assigned to known functions. A number of genes from the transcription and translation machineries as well as from other cellular processes display characteristic eukaryotic signatures or are clearly eukaryote-specific.

Selfish DNA in protein-coding genes of Rickettsia.

Rickettsia conorii, the aetiological agent of Mediterranean spotted fever, is an intracellular bacterium transmitted by ticks. Preliminary analyses of the nearly complete genome sequence of R. conorii have revealed 44 occurrences of a previously undescribed palindromic repeat (150 base pairs long) throughout the genome. Unexpectedly, this repeat was found inserted in-frame within 19 different R. conorii open reading frames likely to encode functional proteins. We found the same repeat in proteins of other Rickettsia species. The finding of a mobile element inserted in many unrelated genes suggests the potential role of selfish DNA in the creation of new protein sequences.

Spastin, a new AAA protein, is altered in the most frequent form of autosomal dominant spastic paraplegia.

Autosomal dominant hereditary spastic paraplegia (AD-HSP) is a genetically heterogeneous neurodegenerative disorder characterized by progressive spasticity of the lower limbs. Among the four loci causing AD-HSP identified so far, the SPG4 locus at chromosome 2p2-1p22 has been shown to account for 40-50% of all AD-HSP families. Using a positional cloning strategy based on obtaining sequence of the entire SPG4 interval, we identified a candidate gene encoding a new member of the AAA protein family, which we named spastin. Sequence analysis of this gene in seven SPG4-linked pedigrees revealed several DNA modifications, including missense, nonsense and splice-site mutations. Both SPG4 and its mouse orthologue were shown to be expressed early and ubiquitously in fetal and adult tissues. The sequence homologies and putative subcellular localization of spastin suggest that this ATPase is involved in the assembly or function of nuclear protein complexes.

[Tamoxifen increases cytotoxic effects of fotemustine. Experimental results on cell lines of human melanoma]. / Le tamoxifène augmente les effets cytotoxiques de la fotémustine. Résultats expérimentaux sur lignées de mélanomes humains.

Fotemustine (Fote) is a new aminoacid linked chloroethyl nitrosourea which has been shown to be useful in disseminated malignant melanoma. The aim of the present study was to analyze the cytotoxic effects resulting from the combination of antiestrogens and Fote on human melanoma cell lines. The antiestrogens tested were tamoxifen (TMX 5.10(-7) M and 5.10(-6) M) and 40H TMX (5.10(-8) M and 5.10(-7) M). As a preliminary step, a series of nine human melanoma cell lines was screened in order to identify and quantify the presence of estradiol receptors (ER) in these cell lines. This led to selecting an ER positive (+) cell line. The drugs alone or in combination were then tested against CAL 1 ER (+) and CAL 7 ER (-) melanoma cell lines. Different sequences of drug combinations were tested using clinically compatible drug concentrations. For CAL 1 cells there was a growth inhibitory effect induced by the antiestrogens given alone. Overall, the presence of the antiestrogens resulted in higher cytotoxic effects than when cells were exposed to Fote alone. The lowest IC50 Fote values as compared to Fote alone were generated by the sequences with the antiestrogens administered before Fote. Significantly, these associations with antiestrogens enabled the IC50 values of Fote to be reduced up to 80%. Globally TMX and 40H TMX had similar synergistic effects. TMX and 40H TMX had a modest influence on Fote cytotoxic effects against CAL 7 ER (-) cells. These data may be useful for optimal planning of future clinical trials for malignant melanoma using antiestrogens and nitrosoureas.

Cytotoxic effects of long-term circulating ultrafiltrable platinum species and limited efficacy of haemodialysis in clearing them.

We applied haemodialysis to clear platinum (Pt) circulating species following renal insufficiency due to an accidental cisplatin overdosage (205 mg/m2 instead of 100 mg/m2). Serum samples were repeatedly obtained during this clinical episode from day 5 up to day 30 after cisplatin dosing. A serum aliquot taken at day 22 after cisplatin administration was tested to assess the possible cytotoxicity exhibited by the circulating Pt species on a head and neck tumour cell line. The profile of ultrafiltrable (UF) Pt during successive haemodialysis cycles was striking. After each haemodialysis cycle, a marked decrease in UF Pt, occurred but was followed by more or less pronounced rebounds. Cisplatin concentration-cytotoxic effect curves obtained in vitro from patient serum before cisplatin administration and healthy control serum exhibited very similar concentration effect profiles. In contrast, the patient serum taken at day 22 after cisplatin administration resulted in marked cytotoxic effects, which were much greater than those which could have been anticipated considering the Pt concentration of this serum sample. The present report underlines the limited usefulness of haemodialysis for rescuing cisplatin treated patients, exhibiting unanticipated postinfusion renal failure with overexposure to the drug. The in vitro investigations suggest that pharmacological effects of Pt derivatives may not only be attributable to short-term effects of the drug diffusion into tissues, but also to more delayed effects from Pt circulating species.

Tamoxifen enhances the cytotoxic effects of the nitrosourea fotemustine. Results on human melanoma cell lines.

Fotemustine (Fote) is a new amino acid-linked chloroethyl nitrosourea which has been shown to be useful in disseminated malignant melanoma. The aim of the present study was to analyse the cytotoxic effects resulting from the combination of anti-oestrogens and Fote on human melanoma cell lines. The anti-oestrogens tested were tamoxifen (TMX, 5 x 10(-7) mol/l and 5 x 10(-6) mol/l) and 4OH TMX (5 x 10(-8) mol/l and 5 x 10(-7) mol/l). As a preliminary step, a series of nine human melanoma cell lines was screened in order to identify and quantify the presence of oestradiol receptors (ER) in these cell lines. This led to the selection of an ER-positive (+) cell line. The drugs alone or in combination were then tested against CAL 1 ER (+) and CAL 7 ER (-) melanoma cell lines. Different sequences of drug combinations were tested using clinically compatible drug concentrations. For CAL 1 cells, there was a growth inhibitory effect induced by the anti-oestrogens given alone. Overall, the presence of the anti-oestrogens resulted in higher cytotoxic effects than when cells were exposed to Fote alone. The lowest IC50 Fote values as compared to Fote alone were generated by the sequences in which the anti-oestrogens were administered before Fote. Significantly, these associations with anti-oestrogens enabled the IC50 values of Fote to be reduced by up to 80%. Globally, TMX and 4OH TMX had similar synergistic effects. TMX and 4OH TMX had a modest influence on Fote cytotoxic effects against CAL 7 ER-negative cells. These data may be useful for optimal planning of future clinical trials for malignant melanoma using anti-oestrogens and nitrosoureas.