Actin-associated proteins in Dictyostelium discoideum

The cellular slime mold Dictyostelium discoideum is becoming the premier system for the explication of the biochemical and cellular events that occur during motile processes. Proteins associated with the actin cytoskeleton, in particular, appear to play key roles in cellular responses to many external stimuli. This review summarizes our present understanding of the actin-associated proteins in Dictyostelium, including their in vitro activities and their structural and/or functional analogues in mammalian cells.     

Identification of multiple cyclic AMP-binding proteins in developing Dictyostelium discoideum cells

We have purified two cAMP-binding proteins from developing Dictyostelium discoideum cells, which we designate as CABP-1 and CABP-2. Purified CABP-1 consists of two polypeptides of Mr 41,000 and 36,000, which we refer to as CABP-1A and CABP-1B, respectively. Although CABP-1 exhibited specificity for cAMP, it was not labeled at a detectable level when mixed with 8-azidoadenosine 3':5'-monophosphate (8-N3[3H]cAMP). Unlike CABP-1, CABP-2 was labeled efficiently with 8-N3[3H]cAMP. Purified CABP-2 has a molecular weight of 41,000 and an isoelectric point of 5.8-6.0. The physical and biochemical properties of CABP-2 suggest that it is the regulatory subunit of cAMP-dependent protein kinase described by others (de Gunzburg, J., Part, D., Guiso, N., and Veron, M. (1984) Biochemistry 23, 3805-3812; Majerfeld, J. H., Leichtling, B. H., Maligeni, J. A., Spitz, E., and Rickenberg, H. V. (1984) J. Biol. Chem. 259, 654-661). Although CABP-1A and CABP-2 have the same molecular weight, they appear to be encoded by different genes. Two-dimensional gel electrophoresis revealed that the two polypeptides had different isoelectric points. Moreover, monoclonal antibodies raised against CABP-1 did not cross-react with CABP-2. Also, in vitro translation followed by immunoprecipitation showed that these two polypeptides were derived from primary translation products. Our finding of a novel cAMP-binding protein, CABP-1, suggests that cAMP-dependent protein kinase may not be the only intracellular regulator mediating the effects of cAMP in developing D. discoideum cells.     

Phosphotyrosine-containing proteins in Dictyostelium discoideum.

Phosphotyrosine-containing proteins in Dictyostelium discoideum were detected by immunoblot analysis and immunoprecipitation using a monoclonal anti-phosphotyrosine antibody. The iodinated antibody recognized on bots a cluster of 205-220 kDa polypeptides and bands of 107 and 60 kDa. The 107 and 60 kDa polypeptides and, in addition, a 82 kDa one became phosphorylated on tyrosine when the immunoprecipitate was incubated with [gamma-32P]ATP. In preparations from differentiating cells the intensity of the label was increased in the 60 kDa band and decreased in the 107 and 205-220 kDa bands.     

Identification and characterization of developmentally regulated mRNP proteins of Dictyostelium discoideum

The isolation of poly(A)+ polysomal and nonpolysomal RNPs by oligo(dT)-cellulose chromatography has led to the identification of more than 20 polypeptides that bind to the poly(A)+ mRNA in growing Dictyostelium cells. Most of these polypeptides were identified in experiments using short-wave UV light (254 nm) to crosslink specifically bound proteins to the RNA. Digestion of the RNPs with ribonucleases A and T1 prior to their application to oligo(dT)-cellulose permitted the isolation of the 3' poly(A)-protein complexes. In polysomal RNPs, two major polypeptides, with molecular weights of 31,000 (p31) and 31,500 (p31.5), are bound to poly(A). These proteins can also be purified from cytoplasmic extracts by affinity chromatography on poly(A)-Sepharose. Partial proteolytic digestion of p31 and p31.5 indicates that they are closely related. The UV-crosslinking experiments established that p31 and p31.5 bind to the non-poly(A) segments of mRNA as well. In nonpolysomal RNPs, p31 and a polypeptide with a molecular weight of 29,500 (p29.5) are the major species associated with poly(A). Partial proteolytic digestion of p29.5 indicates that it is closely related to p31 and p31.5. Only small amounts of p29.5 were observed in the polysomal poly(A)-protein complexes. Early in Dictyostelium development, when cellular translation activity is sharply reduced, most of the p29.5, p31 and p31.5 present is selectively degraded. These observations are consistent with a translational role for these proteins.     

Identification by computer sequence analysis of transcriptional regulator proteins in Dictyostelium discoideum and Serratia marcescens

We have performed computer searches in the database of known protein sequences for proteins similar in sequence to bacteriophage regulatory proteins of known 3-D structure. The searches are more selective than other methods due to the use of a length-dependent threshold in sequence similarity, above which structural homology is implied with high certainty. Two probable DNA binding proteins were identified which are predicted to have a three-dimensional structure very similar to bacteriophage cro and repressor proteins. Approximate three-dimensional model coordinates are available from the authors. Both proteins contain the helix-turn-helix sequence motif typical of a wide class of DNA binding proteins and their function is deduced by analogy to sequence-similar proteins of known function. We predict that the Y.Smal protein in the restriction-modification enzyme gene locus of the enterobacterium serratia marcescens is a regulator of endonuclease expression; and, that the vegetative specific gene VSH7 of the slime mold dictyostelium discoideum codes for a regulator of gene expression specific for the slime mold growth phase before the onset of the developmental program. Point mutations that would have a strong effect on growth regulation phenotype are suggested. The VSH7 protein would be the first eukaryotic representative of the cro/phage repressor class.     

Hypertonicity-induced phosphorylation of proteins in Dictyostelium discoideum

Abstract By exposing the cells of Dictyostelium discoideum to a high concentration (120 mM) of KCl, several species of proteins (188 kilodalton (kDa), 95 kDa, and 71 kDa) are specifically phosphory-lated. This phosphorylation is induced irrespective of the time of starvation of cells by KCl, but not by cAMP, and inhibited by cycloheximide. The ³²P-labeled phosphoryl groups of 95- and 71-kDa proteins disappear by chasing during the subsequent differentiation step in a liquid shake culture. The majority of the 188- and 95-kDa proteins exist in the plasma membrane fraction.     

New actin-binding proteins from Dictyostelium discoideum

Dictyostelium discoideum contains a soluble actin-binding protein that caps actin filaments at their fast growing ends. The purified protein consists of two subunits with 34 kd and 32 kd apparent mol. wts. Like similar proteins from Acanthamoeba and bovine brain the capping protein from D. discoideum acts in a Ca²⁺ -independent manner. It lacks severing activity as indicated by its inability to disrupt the stress fibers and the microfilament network in detergent-extracted cells. Two actin-binding proteins from a plasma membrane-enriched fraction were labeled with [¹²⁵I]actin using a gel overlay technique. One of these proteins, with an apparent mol. wt. of 17 kd in SDS-polyacrylamide gels, has been purified from high-salt extracts, the other protein with an apparent mol. wt. of 31 kd has been purified from Triton X-100 extracted membranes. Monoclonal antibodies were raised against D. discoideum severin, α-actinin, the larger subunit of the capping protein, and the 17-kd membrane-associated protein. Immunoblotting of proteins from whole cell lysates showed that all these actin-binding proteins were present in both growth phase and aggregation-competent cells.     

Endogenous biotinylated proteins in Dictyostelium discoideum.

Biotin-dependent enzymes are involved in carboxylation, decarboxylation and transcarboxylation reactions. Here, we have used sodium dodecyl sulfate polyacrylamide gel electrophoresis and electroblotting followed by probing with avidin to identify biotin-containing polypeptides in Dictyostelium discoideum. Twenty biotinyl polypeptides were visualized, with a 23 kDa protein appearing transiently. Based upon the molecular mobility of the biotinyl polypeptides, D. discoideum may contain the biotin-dependent enzymes acetyl CoA carboxylase, proprionyl CoA carboxylase, pyruvate carboxylase, and 3-methylcrotonyl CoA carboxylase.     

Subcellular distribution of ribosomal proteins in Dictyostelium discoideum

The distribution of ribosomal proteins in monosomes, polysomes, the postribosomal cytosol, and the nucleus was determined during steady-state growth in vegetative amoebae. A partitioning of previously reported cell-specific ribosomal proteins between monosomes and polysomes was observed. L18, one of the two unique proteins in amoeba ribosomes, was distributed equally among monosomes and polysomes. However S5, the other unique protein, was abundant in monosomes but barely visible in polysomes. Of the developmentally regulated proteins, D and S6 were detectable only in polysomes and S14 was more abundant in monosomes. The cytosol revealed no ribosomal proteins. On staining of the nuclear proteins with Coomassie blue, about 18, 7 from 40S subunit and 11 from 60S subunit, were identified as ribosomal proteins. By in vivo labeling of the proteins with [35S]methionine, 24 of the 34 small subunit proteins and 33 of the 42 large subunit proteins were localized in the nucleus. For the majority of the ribosomal proteins, the apparent relative stoichiometry was similar in nuclear preribosomal particles and in cytoplasmic ribosomes. However, in preribosomal particles the relative amount of four proteins (S11, S30, L7, and L10) was two- to four-fold higher and of eight proteins (S14, S15, S20, S34, L12, L27, L34, and L42) was two-to four-fold lower than that of cytoplasmic ribosomes.     

The Dictyostelium discoideum family of Rho-related proteins

Taking advantage of the ongoing Dictyostelium genome sequencing project, we have assembled >73 kb of genomic DNA in 15 contigs harbouring 15 genes and one pseudogene of Rho-related proteins. Comparison with EST sequences revealed that every gene is interrupted by at least one and up to four introns. For racC extensive alternative splicing was identified. Northern blot analysis showed that mRNAs for racA, racE, racG, racH and racI were present at all stages of development, whereas racJ and racL were expressed only at late stages. Amino acid sequences have been analysed in the context of Rho-related proteins of other organisms. Rac1a/1b/1c, RacF1/F2 and to a lesser extent RacB and the GTPase domain of RacA can be grouped in the Rac subfamily. None of the additional Dictyostelium Rho-related proteins belongs to any of the well-defined subfamilies, like Rac, Cdc42 or Rho. RacD and RacA are unique in that they lack the prenylation motif characteristic of Rho proteins. RacD possesses a 50 residue C-terminal extension and RacA a 400 residue C-terminal extension that contains a proline-rich region, two BTB domains and a novel C-terminal domain. We have also identified homologues for RacA in Drosophila and mammals, thus defining a new subfamily of Rho proteins, RhoBTB.     

Identification of an endogenous plasmid in Dictyostelium discoideum

A plasmid has been discovered in a strain of the eukaryote, Dictyostelium discoideum, which has an unstable, non-chromosomal, cobalt resistance phenotype. The plasmid, termed Ddp1, is ˜13.5 kbp in size and is found in the nucleus. It has an A-T content typical of Dictyostelium DNA as judged by its restriction enzyme digestion pattern, and it is not related to either mitochondrial or ribosomal DNA. Similar or identical plasmids have been found in two original, cobalt-sensitive, isolates, NC4 and V12, but no plasmid was detected in three other isolates (WS472, WS526, WS584). The plasmid codes for non-essential functions since it is absent from the latter isolates, and it is lost from mutant strains which are capable of axenic growth.     

Staurosporine induces tyrosine phosphorylation in Dictyostelium discoideum proteins

The treatment of cells with staurosporine results in inhibition and less frequently activation of protein kinases, in a cell-type specific manner. In the social amoeba Dictyostelium discoideum, staurosporine induces marked changes in cell morphology affecting growth and development. Here we describe that incubation of D. discoideum growing or starved cells with staurosporine results in a rapid and unexpected tyrosine phosphorylation on two polypeptides of approximately 64 and approximately 62 kDa. These proteins emerge as novel substrates for tyrosine phosphorylation opening up new perspectives for the study of cell signalling in D. discoideum.     

Identification of proteins responding to adrenergic receptor subtype-specific hypertrophy in cardiomyocytes by proteomic approaches

The individual signaling pathways underlying cardiac hypertrophy, which is induced by either α or β adrenergic receptor (AR), are different. Activation of different AR subtypes couples to different G proteins and induction of specific signaling pathways, which ultimately results in subtype-specific regulation of cardiac function. We present the first proteomics study identifying proteins that are related to AR subtype-specific hypertrophy in cardiomyocytes by comparing the two-dimensional electrophoresis patterns between neonatal rat cardiomyocytes treated by phenylepinephrin (PE) and by isoproterenol (ISO). An improved 2-DE strategy was used in these comparative experiments. Twenty-five differentially expressed proteins in cardiomyocytes treated by PE or treated by ISO were successfully analyzed and identified using matrix-assisted laser desorption/ionization-time of flight mass spectrometry, especially those that might be responsible to intracellular oxidative stress such as dismutase, peroxiredoxin, and thioredoxin-like protein p46. In addition, induced reactive oxygen species were also found to be AR subtype-specifically relevant to endoplasmic reticulum proteinase ERK1/2 phosphorylation during the development of hypertrophy induced by different AR subtypes. The results will help to better understand the underlying mechanisms of different adrenergic receptor subtype-induced hypertrophy.     

Identification of hepatic copper-binding proteins from tilapia by column chromatography with proteomic approaches

Although copper is an essential element, it shows cytotoxic effects when present in excessive amounts with the production of hydroxyl radicals, which can damage phospholipids and enzymes. This necessitates a tight cellular control mechanism for copper homeostasis including its uptake and removal. The high copper contents in the liver of tilapia make this fish a suitable model for the study of copper binding proteins (CBPs). The liver was dissected from tilapia injected with Cu(2+) and cytosolic fractions were separated by using Superdex 75 column chromatography followed by atomic absorption spectrometry. Fractions in two major peaks containing CBPs were analyzed by using differential proteomic approaches, and loaded on a Cu chelating ion-immobilized affinity column (Cu-IMAC). Of the 113 differentially expressed proteins in these two peaks, 28 proteins were found to have copper binding ability, including well-characterized CBPs, such as copper transporter ATP7A and metallothionein. The networks of CBPs built up by Ingenuity Pathway Analysis (IPA) would help us to understand the transportation pathway and function of CBPs, which were related to free radical scavenging, cellular development and lipid metabolism. In addition, our results suggest that Cu(2+) would compete with Fe(2+) and Ca(2+) in binding with some target proteins, such as ferritin, transferrin, and calmodulin.     

Identification of Dictyostelium discoideum plasma membrane proteins by cell surface labeling and quantitative two-dimensional gel electrophoresis

Plasma membrane proteins of the cellular slime mold Dictyostelium discoideum were characterized by two-dimensional polyacrylamide gel electrophoresis using a variety of labeling techniques and a microcomputer-based videodensitometer. Algorithms for the determination of molecular weights and isoelectric points were developed to aid in the comparison of polypeptides from different autoradiographs, Coomassie blue-stained gels, and Western blots. Cell homogenates were compared to plasma membranes isolated by a silica density perturbation technique and to cytoskeletons obtained by nonionic detergent extraction. Plasma membrane proteins were distinguished from subcellular contaminants by lactoperoxidase-catalyzed radioiodination, by selective labeling with N-hydroxysuccinimidyl-2-iminobiotin, and by quantitatively determining the enrichments of individual polypeptides from gels of plasma membrane proteins relative to their counterparts in gels of total cell lysate proteins. In contrast to defining plasma membrane purity by measuring a representative marker enzyme activity, the quantitative two-dimensional gel analysis strategy presented allowed for a rigorous evaluation of the enrichments of all detectable polypeptides in the subcellular fraction. Quantitative two-dimensional gel analysis avoided problems encountered with marker enzyme activation or inhibition during subcellular fractionation as enrichments were based solely on polypeptide amounts. It was also capable of identifying a wider spectrum of plasma membrane proteins than any of the labeling techniques employed in this study. A high resolution two-dimensional gel catalog was generated containing information about plasma membrane protein orientation in the bilayer, association with the cytoskeleton, phosphorylation state, glycosylation state, copy number, isoelectric point, and molecular weight.     

Ribosomal proteins are encoded by single copy genes in Dictyostelium discoideum

Five recombinant plasmids which encode ribosomal proteins (r-proteins) from Dictyostelium discoideum have been isolated. Poly(A) + RNA was size-fractionated by preparative agarose gel electrophoresis and a fraction encoding proteins of less than 35 kDa was used to construct a cDNA library in the plasmid vector pBR322. Individual clones from the library were screened by hybrid-selected translation and those encoding r-proteins were identified by co-migration of the translation products in two-dimensional gel electrophoresis with marker proteins purified from Dictyostelium ribosomes. Initial characterization using the five cDNA plasmids indicates that these r-proteins are encoded by single copy genes and that they are not tightly clustered in the genome.     

The centrosomal component CEP161 of Dictyostelium discoideum interacts with the Hippo signaling pathway

CEP161 is a novel component of the Dictyostelium discoideum centrosome which was identified as binding partner of the pericentriolar component CP250. Here we show that the amino acids 1-763 of the 1381 amino acids CEP161 are sufficient for CP250 binding, centrosomal targeting and centrosome association. Analysis of AX2 cells over-expressing truncated and full length CEP161 proteins revealed defects in growth and development. By immunoprecipitation experiments we identified the Hippo related kinase SvkA (Hrk-svk) as binding partner for CEP161. Both proteins colocalize at the centrosome. In in vitro kinase assays the N-terminal domain of CEP161 (residues 1-763) inhibited the kinase activity of Hrk-svk. A comparison of D. discoideum Hippo kinase mutants with mutants overexpressing CEP161 polypeptides revealed similar defects. We propose that the centrosomal component CEP161 is a novel player in the Hippo signaling pathway and affects various cellular properties through this interaction.