In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors.

Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5'-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds.

KDEL-cargo regulates interactions between proteins involved in COPI vesicle traffic: measurements in living cells using FRET.

How the occupied KDEL receptor ERD2 is sorted into COPI vesicles for Golgi-to-ER transport is largely unknown. Here, interactions between proteins of the COPI transport machinery occurring during a "wave" of transport of a KDEL ligand were studied in living cells. FRET between CFP and YFP fusion proteins was measured by multifocal multiphoton microscopy and bulk-cell spectrofluorimetry. Ligand binding induces oligomerization of ERD2 and recruitment of ARFGAP to the Golgi, where the (ERD2)n/ARFGAP complex interacts with membrane-bound ARF1. During KDEL ligand transport, interactions of ERD2 with beta-COP and p23 decrease and the proteins segregate. Both p24a and p23 interact with ARF1, but only p24 interacts with ARFGAP. These findings suggest a model for how cargo-induced oligomerization of ERD2 regulates its sorting into COPI-coated buds.

Involvement of beta-COP in membrane traffic through the Golgi complex.

Non-clathrin-coated vesicles mediate membrane traffic through the Golgi complex. The proteins that constitute the coats of these vesicles have similar molecular weights to the clathrin coat proteins. A major component of the coat of non-clathrin-coated vesicles, beta-COP, has significant homology with the clathrin coat protein beta-adaptin, indicating that the coats of the two different classes of vesicles may be structurally and functionally homologous.

Organization of desmosomal plaque proteins in cells growing at low calcium concentrations.

Desmosomes are not formed in epithelial cell cultures growing in media with low (less than or equal to 0.1 mM) concentrations of Ca2+ (LCM) but appear rapidly upon shift to media of normal calcium concentrations (NCM). Previous authors using immunolocalization of desmoplakin, a marker protein for the desmosomal plaque, in LCM-grown cells have interpreted positively stained, dense, cytoplasmic aggregates on intermediate filaments (IF) bundles as preformed plaque units which upon NCM shift would move to the plasma membrane and contribute to desmosome formation. Studying various cell cultures, including primary mouse keratinocytes and human A-431 cells, we show that most, probably all, desmoplakin-positive aggregates in LCM-grown cells are associated with membranous structures, mostly vesicles, and also contain other desmosomal markers, including desmoglein, a transmembrane glycoprotein. We interpret such vesicles as residual desmosome-derived domains endocytosed upon cell dissociation. Only keratinocytes grown for long times (2-4 wk) in LCM are practically free from such vesicles. In addition, we demonstrate that certain cells such as A-431 cells, when passaged in LCM and in the absence of stable junctions, are able to continually assemble "half-desmosomes" on the plasma membrane which in turn can be endocytosed as plaque-bearing vesicles. We also show that in LCM the synthesis of several desmosomal proteins (desmoplakins I and II, plakoglobin, desmoglein, "band 6 protein") continues and that most of the plaque protein, desmoplakin, is diffusely spread over the cytoplasm, apparently in a soluble monodisperse form of approximately 9S. From our results we propose that the plaque proteins occur in small, discrete, diffusible entities in the cytoplasm, in concentrations that are relatively high in LCM and low in NCM, from which they assemble directly, i.e., without intermediate precursor aggregates on IFs in the cytoplasm, on certain plasma membrane domains in a Ca2+ dependent process.

Beta-COP localizes mainly to the cis-Golgi side in exocrine pancreas.

We examined the distribution of the non-clathrin-coated vesicle-associated coat protein beta-COP in rat exocrine pancreatic cells by immunogold cytochemistry. Labeling for beta-COP was found in the Golgi region (48%) where it was associated with vesicles and buds of approximately 50 nm, showing a characteristic approximately 10-nm-thick coat. The other half of the label was present in the cytoplasm, not associated with visible coats or membranes, with a minor fraction present on small clusters of tubules and vesicles. Clathrin-coated vesicles were typically located at the trans-side of the Golgi complex, and showed a thicker coat of approximately 18 nm. Of the total beta-COP labeling over the Golgi region, 68% occurred on the cis-side, 6% on the cisternae, 17% on the rims of the cisternae, and only 9% on the trans-side. For clathrin these figures were 16, 2, 4, and 78%, respectively. At the cis-Golgi side beta-COP was present in transitional areas (TA), on so-called peripheral elements (PE), consisting of tubules and vesicles located between the cup-shaped transitional elements (TE) of the RER and the cis-most Golgi cisternae. Label for Sec23p was also present in TA but was located closer to the TE, while beta-COP labeled PE were located near the cis-Golgi cisternae. Upon energy depletion, Golgi associated beta-COP was almost exclusively (86%) in spherical aggregates of 200-500 nm in diameter, whereas the cis-side (6%), the cisternae (1%), the rims (4%) and trans-side (3%) of the Golgi complex, were barely labeled; 50% of the total label remained in the cytoplasm. The aggregates were predominantly located at the cis-side of the Golgi stack, next to, but distinct from the Sec23p positive TA, that were devoid of beta-COP and had only a few recognizable vesicles left. Incubation with aluminum fluoride resulted in fragmentation of the Golgi complex into large clusters of beta-COP positive vesicles, while 50% of the label remained in the cytoplasm, as in control cells. After 10 min of Brefeldin A treatment 91% of beta-COP was cytoplasmic and only 7% associated with membranes of the Golgi complex. The total label for beta-COP over exocrine cells remained unchanged during the incubation with either of the drugs, indicating that the drugs induce reallocation of beta-COP. Our data suggest that beta-COP plays a role in membrane transport at the cis-side of the Golgi complex.

New mutants of Saccharomyces cerevisiae affected in the transport of proteins from the endoplasmic reticulum to the Golgi complex.

We have isolated new temperature-sensitive mutations in five complementation groups, sec31-sec35, that are defective in the transport of proteins from the endoplasmic reticulum (ER) to the Golgi complex. The sec31-sec35 mutants and additional alleles of previously identified sec and vacuolar protein sorting (vps) genes were isolated in a screen based on the detection of alpha-factor precursor in yeast colonies replicated to and lysed on nitrocellulose filters. Secretory protein precursors accumulated in sec31-sec35 mutants at the nonpermissive temperature were core-glycosylated but lacked outer chain carbohydrate, indicating that transport was blocked after translocation into the ER but before arrival in the Golgi complex. Electron microscopy revealed that the newly identified sec mutants accumulated vesicles and membrane structures reminiscent of secretory pathway organelles. Complementation analysis revealed that sec32-1 is an allele of BOS1, a gene implicated in vesicle targeting to the Golgi complex, and sec33-1 is an allele of RET1, a gene that encodes the alpha subunit of coatomer.

Real-time investigation of dynamic protein crystallization in living cells.

X-ray crystallography requires sufficiently large crystals to obtain structural insights at atomic resolution, routinely obtained in vitro by time-consuming screening. Recently, successful data collection was reported from protein microcrystals grown within living cells using highly brilliant free-electron laser and third-generation synchrotron radiation. Here, we analyzed in vivo crystal growth of firefly luciferase and Green Fluorescent Protein-tagged reovirus µNS by live-cell imaging, showing that dimensions of living cells did not limit crystal size. The crystallization process is highly dynamic and occurs in different cellular compartments. In vivo protein crystallization offers exciting new possibilities for proteins that do not form crystals in vitro.

A constitutive transmembrane glycoprotein of Mr 165,000 (desmoglein) in epidermal and non-epidermal desmosomes. II. Immunolocalization and microinjection studies.

Using two monoclonal antibodies described in the preceding paper we determined by immunofluorescence microscopy the distribution of an integral membrane protein of the desmosomal domain, the major glycopolypeptide of Mr 165,000 (bovine muzzle epidermal desmosome band 3; desmoglein) in various normal tissues, tumors and cultured cell lines from several mammalian species. This protein was detected in dotted or streak-like arrays along cell boundary structures which were known to contain non-membrane-integrated desmosomal plaque proteins such as desmoplakins. This is true for epithelial, i.e. cytokeratin-expressing cell types, for the desmin-producing myocardiac and Purkinje fiber cells of the heart, and for certain vimentin-containing cells such as arachnoidal and meningiomal cells and dendritic follicular cells of lymph nodes. However, on the basis of both immunoblot and immunocytochemical reactions, the protein is absent from non-desmosomal adhering junctions, including those devoid of desmoplakin but containing another plaque protein, plakoglobin ("band 5 protein"). We have used these antibodies to localize their epitopes with respect to the cell membrane. By immunoelectron microscopy we found that both epitopes are located in the desmosomal plaques, and this was confirmed by microinjection of purified antibodies into living cultured cells which resulted in labelling of the plaques. From these findings, taken together with previous analyses and localizations of the carbohydrate moieties of this glycoprotein, we conclude that desmoglein is a transmembrane glycoprotein which projects into--and contributes to--the desmosomal plaque structure. This glycoprotein represents a general component of true desmosomes and it is coexpressed with obligatory desmosome-specific plaque proteins such as desmoplakin I. The potential value of this glycoprotein as a desmosomal and cell type marker in histology and tumor diagnosis is discussed.

A constitutive transmembrane glycoprotein of Mr 165,000 (desmoglein) in epidermal and non-epidermal desmosomes. I. Biochemical identification of the polypeptide.

Two murine monoclonal antibodies (DG 3.4 and DG 3.10) raised against a major glycoprotein ("band 3 component") from desmosomes of bovine muzzle epidermis were used in immunoblot experiments following SDS-polyacrylamide gel electrophoresis or two-dimensional gel electrophoresis to identify this or immunologically related proteins in other bovine tissues and cultured cell lines. In all desmosome-bearing cells, i.e. cells also expressing desmoplakins, including representative of stratified, transitional and simple epithelia as well as myocardium, only a single distinct polypeptide of identical Mr value (165,000) and electrical charge was detected. These findings, together with the immunolocalization results reported in the companion paper indicate that this glycoprotein (desmoglein) is a general constituent protein of desmosomes, providing a case of an integral membrane protein co-expressed with non-membranous desmosomal proteins such as the plaque component, desmoplakin I. Our results further suggest that, contrary to previous suggestions, desmoglein is very similar, if not identical in different cells of the same species and does not display significant cell type diversity.

5,6-Dihydrouridine: a marker ribonucleoside for determining whole body degradation rates of transfer RNA in man and rats.

It has previously been demonstrated that N6-threoninocarbonyladenosine is virtually quantitatively excreted in urine. From the similarity of the average molar ratio of 5,6-dihydrouridine to N6-threoninocarbonyladenosine in the urine of human adults (12.6), newborns (12.6) and rats (13.6) with the respective ratio in cytoplasmic tRNA (11.8) we conclude that 5,6-dihydrouridine is also virtually quantitatively excreted in urine. Therefore, excreted 5,6-dihydrouridine is suitable as a marker to assess the whole body degradation rate of tRNA. Relative degradation rates of tRNA determined via excreted 5,6-dihydrouridine in urine are 4.7 times higher in rats (2.2 +/- 0.33 mumol/kg per day) than in human adults (0.48 +/- 0.05 mumol/kg per day) which is similar to the respective difference in the resting metabolic rate per weight unit.

What's new in cytoskeleton-organelle interactions? Relationship between microtubules and the Golgi-apparatus.

Several biochemical processes in animal cells are confined to distinct membrane-bounded compartments. Segregation of specialized functions into different compartments necessitates intercompartment transfer of material. This transfer is mediated by carrier vesicles which, by precise sorting and transport mechanisms, are targetted to their correct destinations. Microtubules, major constituents of the cytoskeleton, are involved both in these intracellular transport processes and in the spatial organization of cytoplasmic organelles. Accumulating evidence suggests that various classes of membranous organelles interact with microtubules. The positioning of several organelles, including the Golgi apparatus and lysosomes, depends on an intact interphase microtubule network. Furthermore, it has been shown that many of these organelles, for example Golgi elements, tubules of the endoplasmic reticulum, exocytic or secretory vesicles and lysosomes move along microtubules. In this article we will discuss the role of microtubules in the movement and positioning of elements of the Golgi complex. The first part will summarize structural and functional aspects of microtubules and the Golgi apparatus and review evidence for their interaction. In the second part, the possible physiological relevance of this interaction will be discussed and correlated with other membrane-microtubule interactions. Finally, emerging questions and perspectives in this field are outlined.

[Enzymatic oxidation reaction in frozen parsley]. / Enzymatische Oxydationsreaktionen in gefrorener Petersilie.

During frozen storage of (non-blanched) parsley, substances are formed showing absorption (234 nm) typical for hydroperoxidienoic acids with conjugated double bonds. However, only small quantities of these compounds are found in the frozen material as compared to other lipid degradation products; for instance, during 2 months at -18 degrees C only 0.1% of the fatty acids (bound to polar lipids) present in fresh parsley are transformed into dienoic acids. These low dienoic acid concentration are nevertheless sufficient to explain off-flavour formation since the sensory threshold values of the degradation products are in the range of some ppb only. After storage for 2 months at -24 degrees C no hydroperoxidienoic acids were found which means that this temperature, in contrast to the usual storage temperature of -18 degrees C, provides practically full protection against lipoxygenase-catalyzed spoiling reactions.

Enzymatic degradation of polar lipids in deep-frozen parsley.

Under the frozen storage at usual storage temperatures of leafy tissues not pretreated by heat, enzymatic lipid degradation reactions take place, which lead already after a few weeks to a considerable or complete loss of the native polar lipids. These degradation processes being accompanied by a deterioration of the flavour have been studied in greater detail in parsley leaves. Among the reaction products we found large amounts of 6-acylmonogalactosyl diglycerides (formed from monogalactosyl diglycerides by enzymatic transacylation) and phosphatidic acid (formed from phospholipids through phospholipase-D action). The generally assumed reaction sequence: formation of free fatty acids by acyl hydrolases followed by hydroperoxidation through lipoxygenase and degradation of the hydroperoxidation through lipoxygenase and degradation of the hydroperoxides into off-flavour compounds may hence take place, if at all, only to a limited extent. Considerable phospholipase D as well as minor acyl transferase activities are detected at --24 degrees C, whereas at --32 degrees C the lipid loss is very low. Deterioration processes can be avoided by blanching, a treatment not leading to any substantial quality loss.

COP I domains required for coatomer integrity, and novel interactions with ARF and ARF-GAP.

We performed a systematic mapping of interaction domains on COP I subunits to gain novel insights into the architecture of coatomer. Using the two-hybrid system, we characterize the domain structure of the alpha-, beta'-, epsilon-COP and beta-, gamma-, delta-, zeta-COP coatomer subcomplexes and identify links between them that contribute to coatomer integrity. Our results demonstrate that the domain organization of the beta-, gamma-, delta-, zeta-COP subcomplex and AP adaptor complexes is related. Through in vivo analysis of alpha-COP truncation mutants, we characterize distinct functional domains on alpha-COP. Its N-terminal WD40 domain is dispensable for yeast cell viability and overall coatomer function, but is required for KKXX-dependent trafficking. The last approximately 170 amino acids of alpha-COP are also non-essential for cell viability, but required for epsilon-COP incorporation into coatomer and maintainance of normal epsilon-COP levels. Further, we demonstrate novel direct interactions of coatomer subunits with regulatory proteins: beta'- and gamma-COP interact with the ARF-GTP-activating protein (GAP) Glo3p, but not Gcs1p, and beta- and epsilon-COP interact with ARF-GTP. Glo3p also interacts with intact coatomer in vitro.

The degradation rates of cytoplasmic tRNA, rRNA and mRNA in rats are elevated after infection with Nippostrongylus brasiliensis.

The effects of a parasitic infection with the nematode Nippostrongylus brasiliensis on the degradation rates of cytoplasmic tRNA, rRNA and mRNA in rats have been investigated by measuring the renal excretion rates of the modified RNA catabolites N6-threoninocarbonyladenosine, pseudouridine and 7-methylguanine. Between days 9 and 13 post-infection when the expulsion of N. brasiliensis is usually the most pronounced, the degradation rates of the different RNA classes were significantly higher than in the control rats (P < 0.05) by, on average, +24% (tRNA), +34% (rRNA) and +26% (mRNA). We suspect that the elevated degradation rates of RNA are related to an increased production of reactive oxygen species by the host during the expulsion of N. brasiliensis.