Yeast aconitase in two locations and two metabolic pathways: seeing small amounts is believing

The distribution of identical enzymatic activities between different subcellular compartments is a fundamental process of living cells. At present, the Saccharomyces cerevisiae aconitase enzyme has been detected only in mitochondria, where it functions in the tricarboxylic acid (TCA) cycle and is considered a mitochondrial matrix marker. We developed two strategies for physical and functional detection of aconitase in the yeast cytosol: 1) we fused the alpha peptide of the beta-galactosidase enzyme to aconitase and observed alpha complementation in the cytosol; and 2) we created an ACO1-URA3 hybrid gene, which allowed isolation of strains in which the hybrid protein is exclusively targeted to mitochondria. These strains display a specific phenotype consistent with glyoxylate shunt elimination. Together, our data indicate that yeast aconitase isoenzymes distribute between two distinct subcellular compartments and participate in two separate metabolic pathways; the glyoxylate shunt in the cytosol and the TCA cycle in mitochondria. We maintain that such dual distribution phenomena have a wider occurrence than recorded currently, the reason being that in certain cases there is a small fraction of one of the isoenzymes, in one of the locations, making its detection very difficult. We term this phenomenon of highly uneven isoenzyme distribution "eclipsed distribution."     

Alkynyl-farnesol reporters for detection of protein S-prenylation in cells

Protein S-prenylation is a lipid modification that regulates membrane-protein and protein-protein interactions in cell signaling. Though sites of protein S-prenylation can be predicted based upon conserved C-terminal CaaX or CC/CXC motifs, biochemical detection of protein S-prenylation in cells is still challenging. Herein, we report an alkynyl-isoprenol chemical reporter (alk-FOH) as an efficient substrate for prenyltransferases in mammalian cells that enables sensitive detection of S-farnesylated and S-geranylgeranylated proteins using bioorthogonal ligation methods. Fluorescent detection alleviates the need to deplete cellular isoprenoids for biochemical analysis of S-prenylated proteins and enables robust characterization of S-prenylated proteins, such as effectors that are injected into host cells by bacterial pathogens. This alkynyl-prenylation reporter provides a sensitive tool for biochemical analysis and rapid profiling of prenylated proteins in cells.     

Rainbow's end: the quest for multiplexed fluorescence quantitative analysis in proteomics

During the past two years, the performance of fluorescence-based protein detection methods has demonstrably eclipsed conventional technologies such as colloidal Coomassie Blue and silver staining with respect to detection sensitivity, quantitative accuracy and compatibility with modern protein identification and characterization procedures. At this point, fluorescence-based methods are poised to offer unprecedented new capabilities in proteomics investigations through the performance of multi-parameter quantitative measurements. The feasibility of such measurements has already been demonstrated through the specific detection of antibiotic-binding proteins, drug-metabolizing enzymes or post-translationally glycosylated proteins, along with the total protein expression profile from electrophoretically separated, complex biological specimens.     

Identification of autophagosome-associated proteins and regulators by quantitative proteomic analysis and genetic screens

Autophagy is one of the major intracellular catabolic pathways, but little is known about the composition of autophagosomes. To study the associated proteins, we isolated autophagosomes from human breast cancer cells using two different biochemical methods and three stimulus types: amino acid deprivation or rapamycin or concanamycin A treatment. The autophagosome-associated proteins were dependent on stimulus, but a core set of proteins was stimulus-independent. Remarkably, proteasomal proteins were abundant among the stimulus-independent common autophagosome-associated proteins, and the activation of autophagy significantly decreased the cellular proteasome level and activity supporting interplay between the two degradation pathways. A screen of yeast strains defective in the orthologs of the human genes encoding for a common set of autophagosome-associated proteins revealed several regulators of autophagy, including subunits of the retromer complex. The combined spatiotemporal proteomic and genetic data sets presented here provide a basis for further characterization of autophagosome biogenesis and cargo selection.     

Characterization of glutamate dehydrogenase isoproteins purified from the cerebellum of normal subjects and patients with degenerative neurological disorders, and from human neoplastic cell lines

Glutamate dehydrogenase (GDH) was purified to homogeneity from cerebellar tissue of three normal subjects and seven patients with four distinct types of degenerative neurological disorders. Nonequilibrium pH gradient gel electrophoresis showed that the purified enzyme consists of four major isoproteins designated GDH 1, 2, 3, and 4. With one exception, the relative abundance and isoelectric points of the GDH isoproteins decrease and the molecular weights increase progressively going from isoprotein 1 to isoprotein 4. The enzyme isolated from the brain of one patient with a variant form of multiple system atrophy displayed marked reduction of GDH isoprotein 1. The Km values of the patients' GDH for alpha-ketoglutarate, glutamate, NADH, and NADPH were significantly increased as compared to GDH obtained from normal and neurologic control subjects. In addition, glutamate levels were reduced markedly in the patient's cerebellum. Pulse-chase studies have shown that both the human hepatoma HepG2 and the human glioma U373 cell lines synthesize exclusively GDH isoprotein 2. The different GDH isoproteins do not have a precursor-product relationship and may represent products of different GDH mRNA species.     

The mechanism of protein kinase C regulation

Protein kinase C (PKC) is a family of serine/threonine protein kinases that plays a central role in transducing extracellular signals into a variety of intracellular responses ranging from cell proliferation to apoptosis. Nine PKC genes have been identified in the human genome, which encode 10 proteins. Each member of this protein kinase family displays distinct biochemical characteristics and is enriched in different cellular and subcellular locations. Activation of PKC has been implicated in the regulation of cell growth and differentiation. This review summarizes works of the past years in the field of PKC biochemistry that covers regulation and activation mechanism of different PKC isoforms.     

Gene response of human monocytic cells for the detection of antimigraine activity of feverfew extracts

The herb feverfew is a folk remedy for various conditions, including inflammation, fever, psoriasis, rheumatism, and asthma. Like many herbal medicines, feverfew's mechanisms of action in the human body are largely unknown and its active ingredients remain elusive. Very often, different extraction methods of herb material produce different physical and biochemical properties and variation in clinical efficacy. We identified 3 major methods of extraction for feverfew aerial parts and used microarray technology to test the hypothesis that extracts produced by different methods elicit different gene expression profiles. We have identified approximately 200 genes that are consistently regulated by the 2 presumptive active antimigraine feverfew extracts but not associated with the inactive extract. Our results suggest that the presumptive active feverfew extracts potently stimulate more genes in human cells than the inactive extracts. We also identified several genes as unique signatures for these active extracts. All 3 feverfew extracts exhibited similar blockades on lipopolysaccharide-mediated TNF-alpha (tumor necrosis factor alpha) release, implicating that TNF-alpha is not responsible for the differences in the effects of the 3 feverfew extracts in human cells. In contrast, the active extracts more effectively suppressed CCL2 (also known as monocyte chemoattractant protein 1, MCP-1) than the inactive extracts, suggesting that CCL2 is a potential cellular target for feverfew's antimigraine effects.     

Regulation of Actin Dynamics in Pollen Tubes: Control of Actin Polymer Level

Actin cytoskeleton undergoes rapid reorganization in response to internal and external cues. How the dynamics of actin cytoskeleton are regulated, and how its dynamics relate to its function are fundamental questions in plant cell biology. The pollen tube is a well characterized actin-based cell morphogenesis in plants. One of the striking features of actin cytoskeleton characterized in the pollen tube is its surprisingly low level of actin polymer. This special phenomenon might relate to the function of actin cytoskeleton in pollen tubes. Understanding the molecular mechanism underlying this special phenomenon requires careful analysis of actin-binding proteins that modulate actin dynamics directly. Recent biochemical and biophysical analyses of several highly conserved plant actin-binding proteins reveal unusual and unexpected properties, which emphasizes the importance of carefully analyzing their action mechanism and cellular activity. In this review, we highlight an actin monomer sequestering protein, a barbed end capping protein and an F-actin severing and dynamizing protein in plant. We propose that these proteins function in harmony to regulate actin dynamics and maintain the low level of actin polymer in pollen tubes.     

Purification of chaperonins

The availability of protein samples of sufficient quality and in sufficient quantity is a driving force in biology and biotechnology. Protein samples that are free of critical contaminants are required for specific assays. Large amounts of highly homogeneous and reproducible material are needed for crystallography and nuclear magnetic resonance studies of protein structure. Protein-based therapeutic factors used in human medicine must not contain any contaminants that might interfere with treatment. The roles played by molecular chaperones in protein folding and in many cellular processes make these proteins very attractive candidates as biochemical reagents, and the class of chaperones called chaperonins is one of the most important candidates. Methods for successfully purifying chaperonins are needed to advance the field of chaperonin-mediated protein folding. This article outlines the strategies and methods used to obtain pure chaperonin samples from different biological sources. The objective is to help new researchers obtain better quality samples of chaperonins from many new organisms.     

Highly divergent amino termini of the homologous human ALR and yeast scERV1 gene products define species specific differences in cellular localization.

The yeast scERV1 gene product is involved in the biogenesis of mitochondria and is indispensable for viability and regulation of the cell cycle. Recently the general importance of this gene for the eukaryotic cell was shown by the identification of a structural and functional human homologue. The homologous mammalian ALR (Augmenter of Liver Regeneration) genes from man, mouse and rat are involved in the phenomenon of liver regeneration. A low expression rate of the genes is found in all investigated cells and mammalian tissues but it is specifically induced after damage of liver organs and is especially high during spermatogenesis. The alignment of the different proteins identifies a highly conserved carboxy terminus with more than 40% identical amino acids between yeast and mammals. The conserved carboxy terminus is functionally interchangeable between distantly related species like yeast and man. In contrast, the amino terminal parts of the proteins display a high degree of variability and significant differences even among closely related species. This finding leads to the problem whether the amino termini have comparable or divergent functions in different species. In this study we demonstrate by heterologous complementation experiments in yeast that the complete human ALR protein with its own amino terminus is not able to substitute for the yeast scERV1 protein. Fusion proteins of Alrp and scErv1p with the green fluorescence protein were created to investigate the respective subcellular localizations of these homologous proteins in yeast and human cells. In yeast cells human Alrp accumulates in the cytoplasm in contrast to yeast scErv1p that is preferentially associated with yeast mitochondria. Comparable studies with human cells clearly show that the homologous human Alrp is located in the cytosol of these cells. Fractionation experiments and antibody tests with yeast and human mitochondria and cellular extracts verify these findings.     

Enzyme activity--it's all about image

Unraveling the functional roles of proteins is a major challenge facing the postgenome researcher. Advances towards this goal have been made through the development of both chemical and biochemical tools for monitoring protein activity. Recently, a myriad of fluorescence-based imaging tools have emerged for in vitro, in vivo and whole animal applications. These tools have provided methods to monitor the spatial and temporal distribution of proteins and bioorganic molecules dynamically. Here, recent advances in chemical and biochemical techniques that allow the detection of enzymatic activity within intact cells and in vivo are reviewed. Such technologies have the potential to be integrated into drug-development programs to facilitate both the functional validation of pharmaceutical targets and the treatment of human disease.     

Rapid assessment of early biophysical changes in K562 cells during apoptosis determined using dielectrophoresis

Apoptosis, or programmed cell death, is a vital cellular process responsible for causing cells to self-terminate at the end of their useful life. Abrogation of this process is commonly linked to cancer, and rapid detection of apoptosis in vitro is vital to the discovery of new anti-cancer drugs. In this paper, we describe the application of the electrical phenomenon dielectrophoresis for detecting apoptosis at very early stages after drug induction, on the basis of changes in electrophysiological properties. Our studies have revealed that K562 (human myelogenous leukemia) cells show a persistent elevation in the cytoplasmic conductivity occurring as early as 30 minutes following exposure to staurosporine. This method therefore allows a far more rapid detection method than existing biochemical marker methods.     

Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21: rationale for a new nomenclature of the S100 calcium-binding protein family

S100 proteins are low-molecular-weight calcium-binding proteins of the EF-hand superfamily and appear to be involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. More than 10 members of the S100 protein family have been described from human sources so far. We have now isolated a YAC clone from human chromosome 1q21, on which 9 different genes coding for S100 calcium-binding proteins could be localized. Moreover, we have mapped the gene coding for S100P to human chromosome 4p16 and thereby completed the chromosomal assignments of all known human S100 genes. The clustered organization of S100 genes in the 1q21 region allows us to introduce a new logical nomenclature for these genes, which is based on the physical arrangement on the chromosome. The new nomenclature should facilitate and further the understanding of this protein family and be easily expandable to other species.     

Bacterial‐type oxygen detoxification and iron‐sulfur cluster assembly in amoebal relict mitochondria

The assembly of vital reactive iron‐sulfur (Fe‐S) cofactors in eukaryotes is mediated by proteins inherited from the original mitochondrial endosymbiont. Uniquely among eukaryotes, however, Entamoeba and Mastigamoeba lack such mitochondrial‐type Fe‐S cluster assembly proteins and possess instead an analogous bacterial‐type system acquired by lateral gene transfer. Here we demonstrate, using immunomicroscopy and biochemical methods, that beyond their predicted cytosolic distribution the bacterial‐type Fe‐S cluster assembly proteins NifS and NifU have been recruited to function within the relict mitochondrial organelles (mitosomes) of Entamoeba histolytica. Both Nif proteins are 10‐fold more concentrated within mitosomes compared with their cytosolic distribution suggesting that active Fe‐S protein maturation occurs in these organelles. Quantitative immunoelectron microscopy showed that amoebal mitosomes are minute but highly abundant cellular structures that occupy up to 2% of the total cell volume. In addition, protein colocalization studies allowed identification of the amoebal hydroperoxide detoxification enzyme rubrerythrin as a mitosomal protein. This protein contains functional Fe‐S centres and exhibits peroxidase activity in vitro. Our findings demonstrate the role of analogous protein replacement in mitochondrial organelle evolution and suggest that the relict mitochondrial organelles of Entamoeba are important sites of metabolic activity that function in Fe‐S protein‐mediated oxygen detoxification.     

Glycosylation diseases: Quo vadis?

About 250 to 500 glycogenes (genes that are directly involved in glycan assembly) are in the human genome representing about 1–2% of the total genome. Over 40 human congenital diseases associated with glycogene mutations have been described to date. It is almost certain that the causative glycogene mutations for many more congenital diseases remain to be discovered. Some glycogenes are involved in the synthesis of only a specific protein and/or a specific class of glycan whereas others play a role in the biosynthesis of more than one glycan class. Mutations in the latter type of glycogene result in complex clinical phenotypes that present difficult diagnostic problems to the clinician. In order to understand in biochemical terms the clinical signs and symptoms of a patient with a glycogene mutation, one must understand how the glycogene works. That requires, first of all, determination of the target protein or proteins of the glycogene followed by an understanding of the role, if any, of the glycogene-dependent glycan in the functions of the protein. Many glycogenes act on thousands of glycoproteins. There are unfortunately no general methods to identify all the potentially large number of glycogene target proteins and which of these proteins are responsible for the mutant phenotypes. Whereas biochemical methods have been highly successful in the discovery of glycogenes responsible for many congenital diseases, it has more recently been necessary to use other methods such as homozygosity mapping. Accurate diagnosis of many recently discovered diseases has become difficult and new diagnostic procedures must be developed. Last but not least is the lack of effective treatment for most of these children and of animal models that can be used to test new therapies.     

Multiple ribonuclease H-encoding genes in the Caenorhabditis elegans genome contrasts with the two typical ribonuclease H-encoding genes in the human genome

Database searches of the Caenorhabditis elegans and human genomic DNA sequences revealed genes encoding ribonuclease H1 (RNase H1) and RNase H2 in each genome. The human genome contains a single copy of each gene, whereas C. elegans has four genes encoding RNase H1-related proteins and one gene for RNase H2. By analyzing the mRNAs produced from the C. elegans genes, examining the amino acid sequence of the predicted protein, and expressing the proteins in Esherichia coli we have identified two active RNase H1-like proteins. One is similar to other eukaryotic RNases H1, whereas the second RNase H (rnh-1.1) is unique. The rnh-1.0 gene is transcribed as a dicistronic message with three dsRNA-binding domains; the mature mRNA is transspliced with SL2 splice leader and contains only one dsRNA-binding domain. Formation of RNase H1 is further regulated by differential cis-splicing events. A single rnh-2 gene, encoding a protein similar to several other eukaryotic RNase H2L's, also has been examined. The diversity and enzymatic properties of RNase H homologues are other examples of expansion of protein families in C. elegans. The presence of two RNases H1 in C. elegans suggests that two enzymes are required in this rather simple organism to perform the functions that are accomplished by a single enzyme in more complex organisms. Phylogenetic analysis indicates that the active C. elegans RNases H1 are distantly related to one another and that the C. elegans RNase H1 is more closely related to the human RNase H1. The database searches also suggest that RNase H domains of LTR-retrotransposons in C. elegans are quite unrelated to cellular RNases H1, but numerous RNase H domains of human endogenous retroviruses are more closely related to cellular RNases H.