Sequence and characterisation of a ribosomal RNA operon fromAgrobacterium vitis

One of the four ribosomal RNA operons (rrnA) from theAgrobacterium vitis vitopine strain S4 was sequenced.rrnA is most closely related to therrn operons ofBradyrhizobium japonicum andRhodobacter sphaeroides and carries an fMet-tRNA gene downstream of its 5S gene, as in the case ofR. sphaeroides. The 16S rRNA sequence of S4 differs from theA. vitis K309 type strain sequence by only one nucleotide, in spite of the fact that S4 and K309 have very different Ti plasmids. The predicted secondary structure of the S4 23S rRNA shows several features that are specific for the alpha proteobacteria, and an unusual branched structure in the universal B8 stem. The 3 ends of the three otherrrn copies of S4 were also cloned and sequenced. Sequence comparison delimits the 3 ends of the four repeats and defines two groups:rrnA/rrnB andrrnC/rrnD.     

Intergenic spacers of rRNA genes in three species of theCynareae (Asteraceae)

Intergenic spacers of the rRNA genes of three species of theCynareae tribe:Cynara cardunculus subsp.scolymus (artichoke),Onopordum acanthium, andO. illyricum were cloned in the plasmid pGEM-7zf(+). Detailed restriction mapping and partial sequencing of the IGSs were carried out. The structural analysis showed a clear diversity betweenCynara andOnopordum, while a high degree of homology was found between the twoOnopordum spp. In all three species a fragment of about 450 bp from the 5 end of 18S to the Acc I site with a high sequence homology was present. Nucleotide sequences upstream from the above mentioned Acc I site show a gradual decrease of homology betweenCynara andOnopordum.     

Evolution of thedec-1 eggshell locus inDrosophila. I. Restriction site mapping and limited sequence comparison in themelanogaster species subgroup

Summary We have analyzed 18 kb of DNA in and upstream of thedefective chorion-1 (dec-1) locus of the eight known species of themelanogaster species subgroup ofDrosophila. The restriction maps ofD. simulans, D. mauritiana, D. sechellia, D. erecta, andD. orena are shown to have basically the restriction map ofD. melanogaster, whereas the maps ofD. teissieri andD. yakuba were more difficult to align. However, the basic amount of DNA and sequence arrangement appear to have been conserved in these species. A small deletion of varying length (65–200 bp) is found in a repeated sequence of the central transcribed region ofD. melanogaster, D. simulans, andD. erecta. Restriction site mapping indicated that thedec-1 gene is highly conserved in themelanogaster species subgroup. However, sequence comparison revealed that the amount of nucleotide and amino acid substitution in the repeated region is much larger than in the 5 translated region. The 5 flanking region showed noticeable restriction site polymorphisms between species. Based on calculations from the restriction maps a dendrogram was derived that supports earlier published phylogenetic relationships within themelanogaster species subgroup except that theerecta-orena pair is placed closer to themelanogaster complex than toD. teissieri andD. yakuba.     

Tamarin polyspecific associations: Forest utilization and stability of mixed-species groups

Niche separation is likely to play a key role in the formation of mixed-species groups. Saddle-backed tamarins (Saguinus fuscicollis) were studied at three sites with different primate communities in northern Bolivia: (1) with red-bellied tamarins,S. labiatus; (2) with emperor tamarins,S. imperator; and (3) without a congeneric species. The degree of association is higher betweenS. labiatus andS. fuscicollis than betweenS. imperator andS. fuscicollis and is related to differences in forest utilization between associating pairs. Niche separation is found to be greater betweenS. labiatus andS. fuscicollis than betweenS. fuscicollis andS. imperator. The mean height and habitat utilization ofS. fuscicollis does not differ greatly across the three sites, nor does the height of tamarins in and out of association. It is concluded that combined with differences in body size and dietary overlap, vertical segregation plays an important role in tamarin polyspecific associations (increasing the potential of both foraging and anti-predatory benefits) and that this is not a consequence of vertical displacement ofS. fuscicollis by its dominant congeners.     

Alkaloids of theSedum acre-group (Crassulaceae)

The 16 species of theSedum acre-group were investigated for the presence of alkaloids. They areS. acre ofS. ser.Acria, S. alpestre, S. annuum, S. apoleipon, S. borissovae, S. euxinum, S. grisebachii, S. laconicum, S. multiceps, S. sexangulare, S. tuberiferum, S. tuberosum, S. ursi, andS. urvillei ofS. ser.Alpestria, S. samium ofS. ser.Samia, andS. litoreum ofS. ser.Litorea. S. acre differs significantly from the other species. It contains sedamine, hydroxy sedamine, and a number of 2,6-disubstituted piperidine alkaloids. The leafy parts of the species ofS. ser.Alpestria, S. ser.Samia, andS. ser.Litorea contain 4 piperidine alkaloids which also occur inS. acre, and in addition 4 pyrrolidine alkaloids not present inS. acre. The composition of the alkaloid fraction agrees with the infrageneric classification (series) based on the hybridization patterns of the species (comparia).     

A molecular systematic study ofCathaya, a relic genus of thePinaceae in China

The systematic position ofCathaya, a relic genus of thePinaceae, was discussed based on therbcL gene sequence. The sequence data were analysed with PAUP and MEGA programs. The great genetic distance value betweenCathaya and any other genus of thePinaceae showed thatCathaya was a distinct and isolated genus. The most parsimonious Fitch tree and neighbor-joining tree showed thatCathaya was distantly related to the clade comprisingAbies, Keteleeria, Pseudolarix andTsuga, and a sister group relationship betweenCathaya andPinus was weakly supported.Pseudotsuga is closely related toLarix. In theAbies-Keteleeria-Pseudolarix-Tsuga clade,Abies has a close relationship toKeteleeria whilePseudolarix is relatively closely related toTsuga.     

Paleobotanical evidence on the early radiation of nonmagnoliid dicotyledons

Paleobotanical studies indicate that several isolated and systematically depauperate groups of extant woody dicotyledons originated in the Mid Cretaceous. TheChloranthaceae had probably differentiated into insect-pollinated (Chloranthus andSarcandra) and wind-pollinated (Ascarina andHedyosmum) forms by the end of the Albian, and leaves referable to theTrochodendrales are known from the Albian and Cenomanian. In the latest Cretaceous and Early Tertiary, extinct representatives of theTrochodendrales includedNordenskioldia and theJoffrea-Nyssidium complex. ThePlatanaceae also differentiated before the end of the Albian and initially had insect-pollinated, unisexual flowers with five carpels or stamens. Some of these features persisted in the platanoid lineage until the Early Tertiary, and during the Paleocene and Eocene thePlatanaceae included forms with elliptical, palmate and pinnate foliage. The history of thePlatanaceae suggests that several features of the reproductive morphology of extant taxa may have arisen in association with a trend toward wind pollination. In the Mid Cretaceous, platanoid foliage partially intergrades with pinnateSapindopsis and pedateDebeya-Dewalquea leaves suggesting a close relationship betweenPlatanaceae andRosidae andFagaceae respectively. TheChloranthaceae, Trochodendrales, andPlatanaceae all occupy a somewhat intermediate position between theMagnoliidae andHamamelidae and are of considerable interest with respect to their role in the initial radiation of nonmagnoliid (higher) dicotyledons.     

TheStreptomyces aureofaciens homologue of thewhiB gene is essential for sporulation; Its expression correlates with the developmental stage

In previous experiments, aStreptomyces aureofaciens gene highly similar to the sporulation-specificwhiB gene ofStreptomyces cœlicolor was identified. By intergrative transformationvia double cross-over, a stable null mutant of thewhiB-homologous gene ofS. aureofaciens was obtained. The disruption blocked differentiation at a stage between the formation of aerial mycelium and the development of mature spores, producing white aerial hyphae without septation. Expression of thewhiB gene was investigated during differentiation by S1 nuclease mapping, using RNA prepared fromS. aureofaciens in various developmental stages. Two putative promoters were identified upstream of thewhiB coding region. The stronger promoter,whiB-P2, was induced at the beginning of aerial mycelium formation, and the weaker promoter,whiB-P1, was expressed fairly constantly during differentiation. No differences in the expression of thewhiB promoters were detected in anrpoZ-disruptedS. aureofaciens strain. The promoter bearing DNA fragment was inserted into the promoter-probe vector pARC1 to produce an expression pattern consistent with the results of direct RNA analysis.     

Phylogenetic depth ofThermotoga maritima inferred from analysis of thefus gene: Amino acid sequence of elongation factor G and organization of theThermotoga str operon

Summary The gene (fus) coding for elongation factor G (EF-G) of the extremely thermophilic eubacteriumThermotoga maritima was identified and sequenced. The EF-G coding sequence (2046 bp) was found to lie in an operon-like structure between the ribosomal protein S7 gene (rpsG) and the elongation factor Tu (EF-Tu) gene (tuf). TherpsG, fus, andtuf genes follow each other immediately in that order, which corresponds to the order of the homologous genes in thestr operon ofEscherichia coli. The derived amino acid sequence of the EF-G protein (682 residues) was aligned with the homologous sequences of other eubacteria, eukaryotes (hamster), and archaebacteria (Methanococcus vannielii). Unrooted phylogenetic dendrogram, obtained both from the amino acid and the nucleotide sequence alignments, using a variety of methods, lend further support to the notion that the (present) root of the (eu)bacterial tree lies betweenThermotoga and the other bacterial lineages.     

Genomic organization of a mouse MHC class II region including theH2-M andLmp2 loci

The region encompassing theMa, Mb1, Mb2, andLmp2 genes of the mouse class II major histocompatibility complex (MHC) was sequenced. Since this region contains clusters of genes required for efficient class I and class II antigen presentation, it was interesting to search for putative additional genes in the 21 kilobase gap between theMb1 andLmp2 genes. Computer predictions of coding regions and CpG islands, exon trapping experiments, and cross-species comparison with the corresponding human sequence indicate that no additional functional gene is present in that stretch. However, computer analysis revealed the possible existence of an alternative 3 exon forMb1. Except for the fact that the mouse MHC contains twoMb genes, the genomic organization of theH2-M loci was found to be almost identical to the organization of the humanHLA-DM genes. The promoter regions of theMa andMb genes also resemble classical class II promoters, containing typical S, X, and Y boxes. Like the human genes, the threeH2-M genes displayed very limited polymorphism when we compared the cDNA sequences from six haplotypes. Finally, comparison ofDMB withMb1 andMb2, both at the genomic level and in their coding regions, suggests that theMb gene was recently duplicated, probably only in certain rodents.     

The white-phase-specific gene<Emphasis Type="Italic"> WH11</Emphasis> is not required for white-opaque switching in<Emphasis Type="Italic"> Candida albicans</Emphasis>

Phenotypic switching between white and opaque cells is important for adaptation to different host environments and for mating in the opportunistic fungal pathogen Candida albicans. Genes that are specifically activated in one of the two cell types are likely to be important for their phenotypic characteristics. The WH11 gene is a white-phase-specific gene that has been suggested to be involved in the maintenance of the white-phase phenotype. To elucidate the role of WH11 in white-opaque switching, we constructed mutants of the C. albicans strain WO-1 in which the WH11 gene was deleted. The wh11 mutants were still able to form both white and opaque cells whose cellular and colony phenotypes were indistinguishable from those of the wild type. Deletion of WH11 also did not affect the activation and deactivation of the white-phase-specific WH11 promoter and the opaque-phase-specific OP4 and SAP1 promoters in the appropriate cell type. Finally, switching from the white to the opaque phase and vice versa occurred with the same frequency in wild-type and wh11 mutants. Therefore, the WH11 gene is not required for phenotypic switching, and its protein product seems to have other roles in white cells, which are dispensable after the switch to the opaque phase.Communicated by E. Cerdá-Olmedo     

Fungal catabolic gene regulation: Molecular genetic analysis of theamdS gene ofAspergillus nidulans

Aspergillus nidulans is an excellent experimental organism for the study of gene regulation. Genetic and molecular analyses oftrans-acting andcis-acting mutations have revealed a complex pattern of regulation involving multiple independent controls. Expression of theamdS gene is regulated by thefacB andamdA genes which encode positively acting regulatory proteins mediating a major and a minor form of acetate induction respectively. The product of theamdR gene mediates omega amino acid induction ofamdS. The binding sites for each of these proteins have been localised throughamdS cis-acting mutations which specifically affect the interaction with the regulatory protein. The global controls of nitrogen metabolite repression and carbon catabolite repression regulate the expression of many catabolic genes, includingamdS. Nitrogen control is exerted through the positively actingareA gene product and carbon control is dependent on thecreA gene product. Each of the characterized regulatory genes encodes a DNA-binding protein which recognises particular sequences in theamdS promoter to activate or repress gene expression. In addition, there is evidence for other genetically uncharacterised proteins, including a CCAAT-binding complex, which interact with the 5 region of theamdS gene.     

Relationships between species ofLeymus,Psathyrostachys, andHordeum (Poaceae,Triticeae) inferred from Southern hybridization of genomic and cloned DNA probes

We have used total genomic DNA as a probe to size-fractionated restriction enzyme digests of genomic DNA from a range ofTriticeae species from the generaLeymus Hochst.,Psathyrostachys Nevski, andHordeum L., and hybrids betweenHordeum andLeymus to investigate their taxonomic relationships. Genomic Southern hybridization was found to be an effective and simple way to assess the distribution and diversity of essentially species-specific and common, repetitive DNA sequences, and is hence especially useful in evolutionary studies. The DNA sequences ofH. vulgare seem to diverge substantially from those ofH. brachyantherum, H. lechleri, H. procerum, andH. depressum. The genome ofThinopyron bessarabicum shows little homology to those of theLeymus species investigated, confirming thatT. bessarabicum is not an ancestral genome inLeymus. Although the genomes ofLeymus andPsathyrostachys share substantial proportions of DNA sequences, they include divergent repeated sequences as well. Hybridization with a ribosomal DNA probe (pTa 71) showed that the coding regions containing structural genes encoding the 18 S, 5.8 S, and 26 S ribosomal RNA were conserved among the species investigated, whereas the intergenic spacer region was more variable, presenting different sizes of restriction fragments and enabling a classification of the species. The rye heterochromatin probe pSc 119.2 hybridized to DNA fromH. lechleri andT. bessarabicum, but not to DNA from the other species investigated.