Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy

The lifecycle, and therefore the virulence, of single-stranded (ss)-RNA viruses is regulated not only by their particular protein gene products, but also by the secondary and tertiary structure of their genomes. The secondary structure of the entire genomic RNA of satellite tobacco mosaic virus (STMV) was recently determined by selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). The SHAPE analysis suggested a single highly extended secondary structure with much less branching than occurs in the ensemble of structures predicted by purely thermodynamic algorithms. Here we examine the solution-equilibrated STMV genome by direct visualization with cryo-electron microscopy (cryo-EM), using an RNA of similar length transcribed from the yeast genome as a control. The cryo-EM data reveal an ensemble of branching patterns that are collectively consistent with the SHAPE-derived secondary structure model. Thus, our results both elucidate the statistical nature of the secondary structure of large ss-RNAs and give visual support for modern RNA structure determination methods. Additionally, this work introduces cryo-EM as a means to distinguish between competing secondary structure models if the models differ significantly in terms of the number and/or length of branches. Furthermore, with the latest advances in cryo-EM technology, we suggest the possibility of developing methods that incorporate restraints from cryo-EM into the next generation of algorithms for the determination of RNA secondary and tertiary structures.     

Nonuniform size distribution of nascent globin peptides, evidence for pause localization sites, and a cotranslational protein-folding model

Examination of nascent globin peptides accumulatingin vitro during globin synthesis in rabbit reticulocyte lysates was carried out. A view was supported that nonrandom distribution of codons with different usage frequencies in mRNA may determine the messenger's translation kinetics. Regions of reduced translation of - and -globin polypeptide chains were localized, and the cotranslational protein-folding model suggested previously was substantiated. An active conjunction of synthesis and folding of proteins was proposed as one of the main destinations of a translation nonuniformity.     

Genetic diversity and population structure in two species of sea cucumber: differing patterns according to mode of development

The population structure of two species of sea cucumber was examined based on mitochondrial DNA sequence analysis. Cucumaria miniata , a species with pelagic nonfeeding larvae lasting less than 2 weeks, and C. pseudocurata , a brooding species lacking a pelagic phase, both occur over similar wide ranges of the northeastern Pacific between Alaska and California. No significant genetic structuring was observed among C. miniata samples with 95% of the observed nucleotide variance attributable to that within population samples. Conversely, only 3.4% of the observed variance was attributed to that within C. pseudocurata population samples, with sampling sites typically greater than 100 km apart. At a finer scale, two C. pseudocurata population samples taken 5 km apart were not statistically different. A significant genetic disjunction was observed among populations of the brooding species, but not in species with pelagic larvae, north of Vancouver Island, Canada, corresponding to the splitting of the California and Alaska currents. Given the observed high levels of genetic diversity in northern samples, this genetic break indicates survival in northern, as well as southern, Pleistocene refugia. These results clearly demonstrate the effects that changes in life-history patterns can have on dispersal, population structure, and the potential for speciation events.     

A novel isotope labeling protocol for bacterially expressed proteins

Summary A novel protocol for isotopically labeling bacterially expressed proteins is presented. This method circumvents problems related to poor cell growth, commonly associated with the use of minimal labeled media, and problems with protein induction encountered, less commonly, when using enriched labeled media. The method involves initially growing the bacterial cells to high optical density in a commercially available enriched labeled medium. Following a suitable growth period, the cells are transferred to a different (minimal) labeled medium, appropriate for induction. The method is demonstrated using the protein melanoma growth stimulating activity (MGSA).     

Ultrastructure and movements of cell structures in normal pea and an ageotropic mutant

The pea mutant (Pisum sativum ageotropum) and the normal pea (P. sativum cv. Sabel) were compared in order to see if there were any differences in root anatomy or submorphology which could explain the presumed ageotropic behaviour of the mutant. In both types the root cap consists of a central core (columella) distinct from the peripheral part. The core contains five to six rows of columella cells, each consisting of 10 to 16 storeys of statocytes. The ultrastructure of the columella cells in the two types is very similar; the main difference is confined to the distribution of rough endoplasmic reticulum (ER), which in the mutant statocytes is evenly distributed throughout the cell, while in the normal pea statocytes it is mainly concentrated in the distal part at the “floor” of the cell. Using light micrographs, the movement of amyloplasts and nuclei have been followed in detail during a 40 min inversion period. The pattern of movement of the amyloplasts is apparently identical in the two types and the distances moved during the inversion period are 39 μm and 44 μm in the normal and mutant statocytes, respectively. The nucleus has not been observed to move in normal pea; a slight rearrangement of the nucleus position can be observed during the period 30 to 40 min after the start of inversion of the mutant. Based on magnified electron micrographs of the statocytes a morphometrical analysis was made of five cell structures – amyloplasts, nuclei, mitochondria, vacuoles and ER – which appeared to be freely movable or redistributable under the influence of the gravitational force.     

Intercellular communication inAzolla roots: II. Electrical coupling

Summary There is a predictable and well defined variation in numbers of plasmodesmata in roots ofAzolla. As the apical cell of the root ages, it lays down walls with progressively fewer plasmodesmata, thereby gradually cutting itself off from the rest of the root (Gunning 1978). Electrical coupling was examined between the apical cell and an adjacent merophyte in roots of various lengths. The apical cell becomes increasingly electrically isolated from the rest of the root as it ages. Electrical coupling is strongly correlated with the number of the plasmodesmata between the coupled cells. The resistance of a plasmodesma, as estimated from equivalent electrical circuits, was 150–600 times more resistive than a value based on theoretical considerations. No evidence was found for a change in the physiology of plasmodesmata as the root ages. Coupling experiments, both on root hairs and at the apex, gave some suggestion that plasmodesmata may be less resistive towards the apical cell than away from it.