Phylogeny of the Rhizobium–Allorhizobium–Agrobacterium clade supports the delineation of Neorhizobium gen. nov.

The genera Agrobacterium, Allorhizobium, and Rhizobium belong to the family Rhizobiaceae. However, the placement of a phytopathogenic group of bacteria, the genus Agrobacterium, among the nitrogen-fixing bacteria and the unclear position of Rhizobium galegae have caused controversy in previous taxonomic studies. To resolve uncertainties in the taxonomy and nomenclature within this family, the phylogenetic relationships of generic members of Rhizobiaceae were studied, but with particular emphasis on the taxa included in Agrobacterium and the “R. galegae complex” (R. galegae and related taxa), using multilocus sequence analysis (MLSA) of six protein-coding housekeeping genes among 114 rhizobial and agrobacterial taxa. The results showed that R. galegae, R. vignae, R. huautlense, and R. alkalisoli formed a separate clade that clearly represented a new genus, for which the name Neorhizobium is proposed. Agrobacterium was shown to represent a separate cluster of mainly pathogenic taxa of the family Rhizobiaceae. A. vitis grouped with Allorhizobium, distinct from Agrobacterium, and should be reclassified as Allorhizobium vitis, whereas Rhizobium rhizogenes was considered to be the proper name for former Agrobacterium rhizogenes. This phylogenetic study further indicated that the taxonomic status of several taxa could be resolved by the creation of more novel genera.     

Will the invasive mussel Mytilus galloprovincialis Lamarck replace the indigenous Perna perna L. on the south coast of South Africa?

The mussel Mytilus galloprovincialis is invasive worldwide, has displaced indigenous species on the west coast of South Africa and now threatens Perna perna on the south coast. We tested the hypothesis that Mytilus will replace Perna by examining changes in their distribution on shores where they co-exist. Total cover, adult density, recruit density, recruit/adult correlations and mean maximum lengths of both species were measured in 2001 at two contrasting sites (Plettenberg Bay and Tsitsikamma) 70 km apart, each including two locations 100 m apart. Cover and density were measured again in 2004. Total mussel abundance was significantly lower in Tsitsikamma, and recruit density was only 17% that of Plettenberg Bay. Abundance and cover increased upshore for Mytilus, but decreased for Perna, giving Mytilus higher adult and recruit density and total cover than Perna in the upper zones. Low shore densities of recruits and adults were similar between species but cover was lower for Mytilus, reflecting its smaller size, and presumably slower growth or higher mortality there. Thus, mechanisms excluding species differed among zones. Recruitment limitation delays invasion at Tsitsikamma and excludes Perna from the high shore, while Mytilus is excluded from the low shore by post-recruitment effects. Recruitment limitation also shapes population structure. Recruit/adult correlations were significant only where adult densities were low, and this effect was species-specific. Thus, at low densities, larvae settle or survive better near adult conspecifics. After 3 years, these patterns remained strongly evident, suggesting Mytilus will not eliminate Perna and that co-existence is possible through partial habitat segregation driven by recruitment limitation of Perna on the high shore and post-settlement effects on Mytilus on the low shore.     

Identification of the first deletion–insertion involving the complete structure of GAA gene and part of CCDC40 gene mediated by an Alu element

Pompe disease is an uncommon autosomal recessive glycogen storage disorder caused by deficiency of acid α-glucosidase. Classic infantile form triggers severe cardiomyopathy, hypotonia, and respiratory failure, leading to death within the first two years of life. The majority of patients with Pompe disease have been reported to have point mutations in the GAA gene. We report the first complex deletion–insertion encompassing the complete structure of GAA gene and a large fragment of the gene CCDC40 in a patient with very severe form of Pompe disease. Sequencing analysis of breakpoints allowed us to determine the potential implication of an Alu repeat in the pathogenic mechanism. We suggest that molecular strategy of Pompe disease should include systematic analysis of large rearrangements.     

Distribution of the triterpenoid saponins and chemotaxonomy of the genus Clematis L. by high-performance liquid chromatography–mass spectrometry

Selected species of the genus Clematis (Ranunculaceae) have been screened for occurrence of triterpenoid saponins by qualitative HPLC-MSⁿ analysis of root and rhizome materials from 18 Clematis samples as well as the whole plant materials of Clematis puberula var. ganpiniana and Clematis terniflora. The HPLC-MSⁿ analysis allowing the detection of 17 oleanolic acid or hederagenin saponins was carried out in the negative selected ion monitoring (SIM) mode. Triterpenoid saponin profiles of these taxa were used for phylogenetic studies, and results are presented as a dendrogram. Huzhangoside B could be unambiguously identified in all analyzed Clematis taxa, as well as in the investigated Ranunculus taxa. The distribution and chemotaxonomic importance of the triterpenoid saponin profile within this genus are discussed.     

Repression by the cI protein of phage λ: in vitro inhibition of RNA synthesis

We have studied the in vitro repression of RNA synthesis by the cI protein of phage λ. We find that highly purified cI protein is an effective and specific repressor of RNA synthesis from the early gene region of λ DNA. Under optimal conditions at least 95% of the early gene RNA synthesis is repressed and this repression is eliminated or severely impaired by the use of λ DNA-carrying operator-type mutations which reduce the binding affinity of the cI protein. Highly effective repression can be demonstrated only through the use of the initiation-inhibitor rifampicin, which presumably, selects “properly” initiated RNA chains; thus we can by-pass in vitro but not yet solve the problem of how the host polymerase initiates specifically in vivo from the immediate-early promoter sites.     

The light-harvesting chlorophyll a/b · protein complex of the green alga Acetabularia mediterranea isolation and characterization of two subunits

In the green alga Acetabularia mediterranea a light-harvesting chlorophyll a/b · protein complex of 67 000 daltons has been found which contains two polypeptide chains of 21 500 and 23 000 daltons. These two polypeptides were isolated on a preparative scale and were further characterized by several different methods. Both polypeptides proved to be very similar. While their amino acid and sugar compositions as well as their immunochemical properties were almost identical the tryptic peptides and the cyanogen bromide fragments of the two polypeptides revealed minor but significant differences. The 67 000-dalton chlorophyll a/b · protein complex and its two polypeptide components were compared to the light-harvesting chlorophyll a/b · protein of higher plants.     

Cryptic species and systematics of the hynobiid salamanders of the Liua–Pseudohynobius complex: Molecular and phylogenetic perspectives

Using mitochondrial DNA sequencing and allozyme electrophoresis, we examined 18 populations of the Liua–Pseudohynobius complex, endemic to China. Based on their phylogenetic affiliation and exhibited fixed allelic differences, the complex comprises at least six species, two of which are previously unknown cryptic species. The complex is clearly divided into two groups, genus Liua including Liua shihi and Liua tsinpaensis, and genus Pseudohynobius including Pseudohynobius flavomaculatus, Pseudohynobius shuichengensis and the two new species. The previously often used genus name Ranodon is inappropriate, because the type species of the genus, Ranodon sibricus, is distantly related to this complex. The species diversity among Chinese hynobiid salamanders are far from being recognized and further effort should be directed at extensive field collection in central and western China.     

Action of β-galactosidase in medium on the Lemna minor (L.) callus polysaccharides

The callus culture of duckweed cultivated on medium containing different concentrations of β-galactosidase was shown to produce the following polysaccharides: pectin lemnan LMC, intracellular AG1, and extracellular AG2 arabinogalactans. The samples of lemnan with 46% galactose residue reduction and 9-46% increased galacturonic acid residue content were obtained at β-galactosidase concentrations of 10⁻³-10⁻¹ mg/mL. The most substantial alterations in the sugar composition of pectin were found to occur in the fraction with a molecular mass of 100-300 kDa. Low concentrations of enzyme failed to influence the sugar composition of intracellular arabinogalactan, whereas high concentrations were shown to decrease the amount of arabinose residues in AG1 and to cause galactan formation. Extracellular galactan was found to be produced on the medium with 10⁻¹ and 1 mg/mL β-galactosidase whereas extracellular arabinogalactan AG2 was shown to be biosynthesized without β-galactosidase or at a β-galactosidase concentration of 10⁻³ mg/mL. Alterations in the sugar composition of polysaccharides were shown to be connected with the increasing activity of α-l-arabinofuranosidase and β-galactosidase, and with the decreasing activity of intracellular polygalacturonase.     

Patterning the dorsal–ventral axis of the wasp Nasonia vitripennis

Regulatory networks composed of interacting genes are responsible for pattern formation and cell type specification in a wide variety of developmental contexts. Evolution must act on these regulatory networks in order to change the proportions, distribution, and characteristics of specified cells. Thus, understanding how these networks operate in homologous systems across multiple levels of phylogenetic divergence is critical for understanding the evolution of developmental systems. Among the most thoroughly characterized regulatory networks is the dorsal–ventral patterning system of the fly Drosophila melanogaster. Due to the thorough understanding of this system, it is an ideal starting point for comparative analyses. Here we report an analysis of the DV patterning system of the wasp, Nasonia vitripennis. This wasp undergoes a mode of long germ embryogenesis that is superficially nearly identical to that of Drosophila, but one that was likely independently derived. We have found that while the expression of genes just prior to the onset of gastrulation is almost identical in Nasonia and Drosophila, both the upstream network responsible for generating this pattern, and the downstream morphogenetic movements that it sets in motion, are significantly diverged. From this we conclude that many network structures are available to evolution to achieve particular developmental ends.     

Spiroplasma infection in Drosophila melanogaster: What is the advantage of killing males?

Male-killing bacteria are maternally inherited agents that cause death of sons of infected females. Their transmission rate is commonly high but imperfect and also sensitive to different environmental factors. Therefore, the proportion of infected females should be reduced in each generation. In order to explain male-killers spread and persistence in host population, a mechanism resulting in the relative increase of infected females must outweigh the losses caused by the imperfect transmission. The resource release hypothesis states that the males’ death results in increased resources available to sibling females which would otherwise be used by their male siblings. Infected females are then expected: to be larger than uninfected females in natural populations; or to have higher viability; or to have shorter development times; or any combination of these outcomes. Here, we tested the resource release hypothesis by measuring body size of infected and uninfected wild-caught Drosophila melanogaster females and carried out other fitness related measures in the laboratory. Wild-caught infected females produced more daughters than uninfected females in their first days in the laboratory. However, although no significant difference in viability was found in a controlled experiment with infected and uninfected flies from a standard laboratory strain, there was a decrease in development time probably mediated by reduced competition. Fitness effects conditioned by the host genetic background are pointed out as a possible explanation for this difference between wild and laboratory flies. Our findings are discussed in the context of the resource advantage hypothesis.     

Hormonal aspects of oögenesis in the flies Phormia regina and Sarcophaga bullata

The corpora allata (CA) and median neurosecretory cells (MNC) of Phormia regina and Sarcophaga bullata become active with increasing age of the fly, on a diet of sugar alone. To prevent or retard oögenesis the CA or MNCs must be removed shortly after emergence, with subsequent protein meals. Topical JH application partially compensates for CA or MNC removal. This shows that the MNC activate the CA, and not vice versa. The trauma of either operation slightly depresses egg development.Injection of ecdysone into both species in the stage of initial yolk deposition causes the primary oöcytes to degenerate. This leads to development of the penultimate oöcytes. Older and younger egg stages are not sensitive to ecdysone. In P. regina the application of JH to females with developing primary oöcytes stimulates yolk deposition in the penultimate oöcytes.     

E. coli sabotages the in vivo production of O-linked β-N-acetylglucosamine-modified proteins

The O-linked β-N-acetylglucosamine (O-GlcNAc) post-translational modification is an important, regulatory modification of cytosolic and nuclear enzymes. To date, no 3-dimensional structures of O-GlcNAc-modified proteins exist due to difficulties in producing sufficient quantities with either in vitro or in vivo techniques. Recombinant co-expression of substrate protein and O-GlcNAc transferase in Escherichia coli was used to produce O-GlcNAc-modified domains of human cAMP responsive element-binding protein (CREB1) and Abelson tyrosine-kinase 2 (ABL2). Recombinant expression in E. coli is an advantageous approach, but only small quantities of insoluble O-GlcNAc-modified protein were produced. Adding β-N-acetylglucosaminidase inhibitor, O-(2-acetamido-2-dexoy-d-glucopyranosylidene)amino-N-phenylcarbamate (PUGNAc), to the culture media provided the first evidence that an E. coli enzyme cleaves O-GlcNAc from proteins in vivo. With the inhibitor present, the yields of O-GlcNAc-modified protein increased. The E. coli β-N-acetylglucosaminidase was isolated and shown to cleave O-GlcNAc from a synthetic O-GlcNAc-peptide in vitro. The identity of the interfering β-N-acetylglucosaminidase was confirmed by testing a nagZ knockout strain. In E. coli, NagZ natively cleaves the GlcNAc-β1,4-N-acetylmuramic acid linkage to recycle peptidoglycan in the cytoplasm and cleaves the GlcNAc-β-O-linkage of foreign O-GlcNAc-modified proteins in vivo, sabotaging the recombinant co-expression system.     

On the structure of the lipopolysaccharide core in the cell wall of Escherichia coli K12 W2252-11U− and its ter-mutant cells

From Escherichia coli K12 W2252-11U^? (wild type I and II) and its Ter-mutants, lipopolysaccharides were isolated and the primary structure of its core region was elucidated, the configuration of the glucose III (1→2)-linked to the glucose II residue in the core of parents (wild type I and II) changes into the configuration of the glucose (1→3)-linkage by the Ter-mutation. Also, the structure of the core in the Ter-15 mutant differs from that in the parent (wild type I) and is similar to that in Escherichia coli C used as an indicator for φ×174 phage. D-ribose residue in the core of the Ter-21 mutant links to the glucose I residue instead of the galactose residue in the core of the parent (wild type II).     

A Comparison of the Membrane Binding Properties of C1B Domains of PKCγ, PKCδ, and PKC?

The C1 domains of classical and novel PKCs mediate their diacylglycerol-dependent translocation. Using fluorescence resonance energy transfer, we studied the contribution of different negatively charged phospholipids and diacylglycerols to membrane binding. Three different C1B domains of PKCs were studied (the classical γ, and the novel δ and ?), together with different lipid mixtures containing three types of acidic phospholipids and three types of activating diacylglycerols. The results show that C1Bγ and C1B? exhibit a higher affinity to bind to vesicles containing 1-palmitoyl-2-oleoyl-sn-phosphatidic acid, 1-palmitoyl-2-oleoyl-sn-phoshatidylserine, or 1-palmitoyl-2-oleoyl-sn-phosphatidylglycerol, with C1B? being the most relevant case because its affinity for POPA-containing vesicles increased by almost two orders of magnitude. When the effect of the diacylglycerol fatty acid composition on membrane binding was studied, the C1B? domain showed the highest binding affinity to membranes containing 1-stearoyl-oleoyl-sn-glycerol or 1,2-sn-dioleoylglycerol with POPA as the acidic phospholipid. Of the three diacylglycerols used in this study, 1,2-sn-dioleoylglycerol and 1-stearoyl-oleoyl-sn-glycerol showed the highest affinities for each isoenzyme, whereas 1,2-sn-dipalmitoylglycerol; showed the lowest affinity. DSC experiments showed this to be a consequence of the nonfluid conditions of 1,2-sn-dipalmitoylglycerol;-containing systems.     

Configuration of the carotenoid in the reaction centers of photosynthetic bacteria. Comparison of the resonance Raman spectrum of the reaction center of Rhodopseudomonas sphaeroides G1C with those of cis-trans isomers of β-carotene

The resonance Raman spectrum of the reaction center of Rhodopseudomonas sphaeroides G1C as well as those of the cis-trans isomers of β-carotene (all-trans, 9-cis, 13-cis, 15-cis and 9-cis, 13-cis- (or 9-cis, 13′-cis)) have been recorded at liquid N₂ temperature by use of the 457.9, 488.0 and 514.5 nm excitation lines. Comparison of the spectra indicated that the carotenoid in the reaction center takes the 15-cis configuration.     

Quality evaluation of Semen persicae (seed of Prunus persica L. Batsch) by gas chromatography–mass spectrometry

Seeds of Prunus persica L. Batsch were collected at various times from different regions of China. The fatty acid composition of the seeds was analysed using gas chromatography-mass spectrometry (GC-MS). The aim was to evaluate whether genetic and environmental factors influenced the chemical profile of fatty acids in Semen persicae. Saturated and unsaturated fatty acids were present at 4.8-8.7% and 90.7-94.8% of total fatty acids, respectively. Oleic and linoleic acids were dominant in all samples and ranged from 59.3 to 81.4% and from 11.6 to 31.0%, respectively. All samples had high levels of unsaturated fatty acids. Hierarchical clustering analysis and principal components analysis were performed to differentiate and classify the samples based on the contents of the characteristic fatty acid constituents. This study provides evidence that metabolites may reflect genetic and environmental similarities, such as management practices used in cultivars (irrigation, fertilization and sanitary treatments), and evidence of the variability of genetic make up and local environmental conditions in samples grown in the wild.     

α-Glucosidase at the tip of the contact chemosensory seta of the blowfly, Phormia regina

α-Glucosidase activity was detected at the tip of the labellar contact chemosensory hair of the blowfly, Phormia regina. The enzyme split about 1 pmole of sucrose per hr per hair on average and the Michaelis constant for sucrose was about 50 mM. The activity of the enzyme was not solubilized into the incubation solution, but stuck stably to the tip of the sensory hair. From the cut end of the sensory hair a high activity of α-glucosidase eluted out. But its Michaelis constant was smaller by far than the one at the tip, suggesting that different types of α-glucosidase isozymes exist in the hair. The possibility that the enzyme at the tip of the sensory hair could be the sugar receptor is discussed.