The NUG1 GTPase reveals and N-terminal RNA-binding domain that is essential for association with 60 S pre-ribosomal particles

The putative yeast GTPase Nug1, which is associated with several pre-60 S particles in the nucleolus and nucleoplasm, consists of an N-terminal domain, which is found only in eukaryotic orthologues, and middle and C-terminal domains that are conserved throughout eukaryotes, bacteria, and archaea. Here, we analyzed the role of the eukaryote-specific Nug1 N-domain (Nug1-N). We show that the essential Nug1-N is sufficient and necessary for nucle(ol)ar targeting and association with pre-60 S particles. Nug1-N exhibits RNA binding activity and is genetically linked in an allele-specific way to the pre-60 S factors Noc2, Noc3, and Dbp10. In contrast, the middle domain, which exhibits a circularly permuted GTPase fold and an intrinsic GTP hydrolysis activity in vitro, is not essential for cell growth. The conserved Nug1 C-domain, which has a yet uncharacterized fold, is also essential for ribosome biogenesis. Our findings suggest that Nug1 associates with pre-60 S subunits via its essential N-terminal RNA-binding domain and exerts a non-essential regulative role in pre-60 S subunit biogenesis via its central GTPase domain.     

SlyD proteins from different species exhibit high prolyl isomerase and chaperone activities

SlyD is a putative folding helper protein from the Escherichia coli cytosol, which consists of an N-terminal prolyl isomerase domain of the FKBP type and a presumably unstructured C-terminal tail. We produced truncated versions without this tail (SlyD) for SlyD from E. coli, as well as for the SlyD orthologues from Yersinia pestis, Treponema pallidum, Pasteurella multocida, and Vibrio cholerae. They are monomeric in solution and unfold reversibly. All SlyD variants catalyze the proline-limited refolding of ribonuclease T1 with very high efficiencies, and the specificity constants (kcat/KM) are equal to approximately 10(6) M(-1) s(-1). These large values originate from the high affinities of the SlyD orthologues for unfolded RCM-T1, which are reflected in low KM values of approximately 1 microM. SlyD also exhibits pronounced chaperone properties. Permanently unfolded proteins bind with high affinity to SlyD and thus inhibit its prolyl isomerase activity. The unfolded protein chains do not need to contain proline residues to be recognized and bound by SlyD. The conservation of prolyl isomerase activity and chaperone properties within the SlyD family suggests that these proteins might act as true folding helpers in the bacterial cytosol. The SlyD proteins are also well suited for biotechnological applications. As fusion partners they facilitate the refolding and increase the solubility of aggregation-prone proteins such as the gp41 ectodomain fragment of HIV-1.     

Sequence diversity of the peptaibol antibiotic suzukacillin-A from the mold Trichoderma viride.

From the culture broth of the mold Trichoderma viride, strain 63 C-I, the polypeptide antibiotic suzukacillin (SZ) was isolated. A peptide mixture named SZ-A was obtained by crystallization from crude SZ. Individual peptides from SZ-A were isolated by semipreparative HPLC and sequences were determined by HPLC-ESI-MS. The data confirm a general sequence of SZ-A published previously and in addition establish the individual sequences of 15 acetylated eicosa peptides with C-terminal alcohols. The major peptide SZ-A4 (21% of all peptides) shows the sequence:Ac-Aib-Ala-Aib-Ala-Aib-Ala(6)-Gln-Aib-Lx(9)-Aib-Gly-Aib(12)-Aib-Pro-Vx(15)-Aib-Vx(17)-Gln-Gln-Fol. Amino acid exchanges of the peptaibol are located in position 6 (Ala/Aib), 9 (Vx/Lx), 12 (Aib/Lx), 17 (Aib/Vx) and possibly at position15 (Val/Iva) (uncommon abbreviations: Aib (alpha-aminoisobutyric acid); Iva (D-isovaline); Lx (L-leucine or L-isoleucine); Vx (L-valine or D-isovaline); Fol (L-phenylalaninol)).     

The larval development of the telotrophic meroistic ovary in the bug Dysdercus intermedius (Heteroptera, Pyrrhocoridae)

Bug ovaries are of the telotrophic meroistic type. Nurse cells are restricted to the anterior tropharium and are in syncytial connection with the oocytes via the acellular trophic core region into which cytoplasmic projections of oocytes and nurse cells open. The origin of intercellular connections in bug ovaries is not well understood. In order to elucidate the cellular processes underlying the emergence of the syncytium, we analysed the development of the ovary of Dysdercus intermedius throughout the five larval instars. Up to the third instar, the germ cell population of an ovariole anlage forms a single, tight rosette. In the center of the rosette, phosphotyrosine containing proteins and f-actin accumulate. This center is filled with fusomal cytoplasm and closely interdigitating cell membranes known as the membrane labyrinth. With the molt to the fourth instar germ cells enhance their mitotic activity considerably. As a rule, germ cells divide asynchronously. Simultaneously, the membrane labyrinth expands and establishes a central column within the growing tropharium. In the fifth instar the membrane labyrinth retracts to an apical position, where it is maintained even in ovarioles of adult females. The former membrane labyrinth in middle and posterior regions of the tropharium is replaced by the central core to which nurse cells and oocytes are syncytially connected. Germ cells in the most anterior part of the tropharium, i.e. those in close proximity to the membrane labyrinth remain proliferative. The posterior-most germ cells enter meiosis and become oocytes. The majority of the ovarioles' germ cells, located in between these two populations, endopolyploidize and function as nurse cells. We conclude that the extensive multiplication of germ cells and their syncytial assembly during larval development is achieved by incomplete cytokineses followed by massive membrane production. Membranes are degraded as soon as the trophic core develops. For comparative reasons, we also undertook a cursory examination of early germ cell development in Dysdercus intermedius males. All results were compatible with the known basic patterns of early insect spermatogenesis. Germ cells run through mitotic and meiotic divisions in synchronous clusters emerging from incomplete cytokineses. During the division phase, the germ cells of an individual cluster are connected by a polyfusome rich in f-actin.     

Selecting normalization genes for small diagnostic microarrays

Background  

Normalization of gene expression microarrays carrying thousands of genes is based on assumptions that do not hold for diagnostic microarrays carrying only few genes. Thus, applying standard microarray normalization strategies to diagnostic microarrays causes new normalization problems.     

Citrulline immunohistochemistry for demonstration of NOS activity in vivo and in vitro.

Nitric oxide (NO), a biomolecule with major cytotoxic potency, is generated by NO synthases (NOS) utilizing l-arginine as substrate and citrulline is formed as a "side product." In brain tissue, citrulline is considered to be produced exclusively by NOS, due to the incomplete urea cycle in the brain. We aimed to characterize NOS activity by citrulline immunostaining in different cell types of the brain under in situ conditions and in slice and culture experiments. NOS-positive neurons and activated microglial cells were the most prominent citrulline-positive structures. Lack of citrulline immunoreaction in neurons of nNOS knockout mice emphasizes the dependency of citrulline positivity on NOS activity, and likewise there was no citrulline staining after application of the NOS inhibitors 7-nitroindazole and NIL. Interestingly, only a portion of NOS-containing neurons costained for citrulline. The inhibition of argininosuccinate synthetase by alpha-methyl-dl-aspartate increased the number of citrulline-positive cells, apparently due to reduction of the turnover rate of citrulline. Cells positive for NOS but negative for citrulline may indicate that the enzyme is either not activated or inhibited by cellular control mechanisms. The fact that not all citrulline-positive cells were NOS positive may be explained by an insufficient detection sensitivity or by disparate sites of citrulline production and recycling. The present results show that citrulline immunocytochemistry offers a viable and convenient means for studying NOS activity at the single-cell level to elicit its posttranslational control under physiological and pathophysiological conditions.     

Root systems of chaparral shrubs

Summary Root systems of chaparral shrubs were excavated from a 70 m² plot of a mixed chaparral stand located on a north-facing slope in San Diego County (32°54 N; 900 m above sea level). The main shrub species present were Adenostoma fasciculatum, Arctostaphylos pungens, Ceanothus greggii, Erigonum fasciculatum, and Haplopappus pinifolius. Shrubs were wired into their positions, and the soil was washed out beneath them down to a depth of approximately 60 cm, where impenetrable granite impeded further washing and root growth was severely restricted. Spacing and interweaving of root systems were recorded by an in-scale drawing. The roots were harvested in accordance to their depths, separated into diameter size classes for each species, and their dry weights measured. Roots of shrubs were largely confined to the upper soil levels. The roots of Eriogonum fasciculatum were concentrated in the upper soil layer. Roots of Adenostoma fasciculatum tended to be more superficial than those from Ceanothus greggii. It is hypothesized that the shallow soil at the excavation site impeded a clear depth zonation of the different root systems. The average dry weight root:shoot ratio was 0.6, ranging for the individual shrubs from 0.8 to 0.4. The root area always exceeded the shoot area, with the corresponding ratios ranging from 6 for Arctostaphylos pungens to 40 for Haplopappus pinifolius. The fine root density of 64 g dry weight per m² under the canopy was significantly higher than in the unshaded area. However, the corresponding value of 45 g dry weight per m² for the open ground is still high enough to make the establishment of other shrubs difficult.     

Transcutaneous measurement of renal function in conscious mice

Determination of glomerular filtration rate (GFR) in conscious mice is cumbersome for the experimenter and stressful for the animals. Here we report on a simple new technique allowing the transcutaneous measurement of GFR in conscious mice. This approach extends our previously developed technique for rats to mice. The technique relies on a miniaturized device equipped with an internal memory that permits the transcutaneous measurement of the elimination kinetics of the fluorescent renal marker FITC-sinistrin. This device is described and validated compared with FITC-sinistrin plasma clearance in healthy, unilaterally nephrectomized and pcy mice. In summary, we describe a technique allowing the measurement of renal function in freely moving mice independent of blood or urine sampling as well as of laboratory assays.     

High-resolution proteomics unravel architecture and molecular diversity of native AMPA receptor complexes

AMPA-type glutamate receptors (AMPARs) are responsible for a variety of processes in the mammalian brain including fast excitatory neurotransmission, postsynaptic plasticity, or synapse development. Here, with comprehensive and quantitative proteomic analyses, we demonstrate that native AMPARs are macromolecular complexes with a large molecular diversity. This diversity results from coassembly of the known AMPAR subunits, pore-forming GluA and three types of auxiliary proteins, with 21 additional constituents, mostly secreted proteins or transmembrane proteins of different classes. Their integration at distinct abundance and stability establishes the heteromultimeric architecture of native AMPAR complexes: a defined core with a variable periphery resulting in an apparent molecular mass between 0.6 and 1 MDa. The additional constituents change the gating properties of AMPARs and provide links to the protein dynamics fundamental for the complex role of AMPARs in formation and operation of glutamatergic synapses.