Frequent Assembly of Chimeric Complexes in the Protein Interaction Network of an Interspecies Yeast Hybrid

Hybrids between species often show extreme phenotypes, including some that take place at the molecular level. In this study, we investigated the phenotypes of an interspecies diploid hybrid in terms of protein–protein interactions inferred from protein correlation profiling. We used two yeast species, Saccharomyces cerevisiae and Saccharomyces uvarum, which are interfertile, but yet have proteins diverged enough to be differentiated using mass spectrometry. Most of the protein–protein interactions are similar between hybrid and parents, and are consistent with the assembly of chimeric complexes, which we validated using an orthogonal approach for the prefoldin complex. We also identified instances of altered protein–protein interactions in the hybrid, for instance, in complexes related to proteostasis and in mitochondrial protein complexes. Overall, this study uncovers the likely frequent occurrence of chimeric protein complexes with few exceptions, which may result from incompatibilities or imbalances between the parental proteomes.     

Chimeric Protein Engineering

Protein stability can be enhanced by the incorporation of non-natural amino acids and semi-rigid peptidomimetics to lower the entropic penalty upon protein folding through preorganization. An example is the incorporation of aminoisobutyric acid (Aib, α-methylalanine) into proteins to restrict the Φ and Ψ backbone angles adjacent to Aib to those associated with helix formation. Reverse-turn analogs were introduced into the sequences of HIV protease and ribonuclease A that enhanced their stability and retained their native enzymatic activity. In this work, a chimeric protein, design_4, was engineered, in silico, by replacing the C-terminal helix of full sequence design protein (FSD-1) with a semi-rigid helix mimetic. Residues 1–16 of FSD-1 was ligated in silico with the N-terminus of a phenylbipyridyl-based helix mimetic to form design_4. The designed chimeric protein was stable and maintained the designed fold in a 100-nanosecond molecular dynamics simulation at 280 K. Its β-hairpin adopted conformations that formed three additional hydrogen bonds. Compared to FSD-1, design_4 contained fewer peptide bonds and internal degrees of freedom; it should, therefore, be more resistant to proteolytic degradation and denaturation.     

Homologous and Hybrid Complexes of Anthranilate Synthase from Bacillus Species

The subunits of anthranilate synthase were separated and partially purified by Sephadex G-100 gel filtration from the following six species of Bacillus: Bacillus subtilis, Bacillus licheniformis, Bacillus alvei, Bacillus coagulans, Bacillus pumilus, and Bacillus mascerans. Our data suggest that the enzyme from B. alvei is unique among these species. First, the anthranilate synthase complexes are readily dissociated during gel filtration in the absence of glutamine into a large component (aminotransferase), subunit E, and a small component subunit X (glutamine-binding protein), whereas a higher salt concentration is required to dissociate the complex from B. alvei. Second, the aminotransferase activity from all six species is stimulated by glycerol and inhibited by tryptophan; however, only the large component from B. alvei is stimulated by 2-mercaptoethanol. Finally, the large component can be titrated with the small component to yield a complex which can utilize glutamine as a substrate (amidotransferase). The homologous complexes have an amidotransferase to aminotransferase ratio of 1.4 to 2.3, but the B. alvei complex has a ratio of 0.9. Except for complexes that involve the large component from B. alvei, hybrid complexes can be formed which have ratios as good as the homologous complexes. These data are consistent with the hypothesis that B. alvei is unique among the bacilli with respect to some enzymes in the aromatic amino acid biosynthetic pathway.     

Protein Synthesis in Hybrid Cells Derived from Fetal Rat × Mouse Chimeric Organs

Abstract. Malignant hybrid cells (As3) derived from fusion of rat hepatoma cells (Fu5AH) with mouse teratocarcinoma cells (OTT6050) were injected into genetically marked mouse blastocysts which were subsequently transferred into pseudopregnant surrogate mothers. From a total of 61 fetuses developed, four normally differentiated fetuses at day 18 of gestation showed hybrid cell contributions in their livers and a few other organs of endo-mesodermal origin. The chimeric tissues were briefly cultured in vitro and then further investigated for their protein synthesis using two-dimensional gel electrophoresis. After comparison of the protein patterns obtained from the corresponding normal rat and mouse organs, several rat-specific polypeptides were detected in the cultured chimeric tissues illustrating functional xenogeneic gene expression during in situ differentiation. In addition, some other rat proteins characteristic of the parental hybrid cell line disappeared. The tumorigenicity of the chimeric tissues was tested by subcutaneous transplantation into immunodeficient nude mice. Tumors originating from two of the four chimeric organs differed histologically from those formed by cells of the hybrid As3 line since they also contained muscle-like structures resembling rhabdomyosarcomas. The tumors were analyzed for their protein synthesis and compared with the three malignant cell lines of parental origin. The morphologic differences between the tumors derived from the chimeric organs and those developed from the As3 cell line were also reflected in characteristic differences of their protein synthesis patterns. Our results demonstrate that interspecific rat × mouse hybrid cells, when implanted into early mouse embryos, participate in fetal tissue differentiation and selectively repress certain rat gene products typical of the malignant parental cells as well as functionally reactivate other rat genes presumably required for normal development.     

Novel Chimeric Peptide Inhibits Protein Kinase C and Induces Apoptosis in Human Immune Cells

Protein kinase C (PKC) participates in a myriad of cellular processes. Protein kinase C isoforms play different roles based on their cellular expression balance and activation. The activity of classical PKC isoforms has been shown to be crucial for immune cell population homeostasis, playing a positive role in survival and proliferation. Protein kinase C inhibitors have been used for conditions where up-regulated PKC results in a pathological state. The most commonly investigated PKC inhibitors are highly effective in inhibiting PKC function but they are relatively unspecific, some of them even inhibiting other kinase families. Protein kinase C pseudosubstrates are auto-inhibitory domains which have been used to inhibit more specifically PKC in vitro but they do not freely penetrate cells. This could be resolved by using cell-permeable PKC pseudosubstrates which would more accurately modulate cellular PKC activity and PKC-related functions in intact cells. Here we show the development of a chimeric peptide inhibitor of classical PKC isoforms, consisting of a cell permeable sequence and a pseudosubstrate sequence which was able to translocate into cells, inhibiting PKC kinase activity and PKC T-cell-specific substrate phosphorylation. We also demonstrate a dramatic reduction in T-cell proliferation at high chimeric peptide concentration; this was attributed to apoptosis induction, as demonstrated by cell shrinking, phosphatidylserine exposure and DNA fragmentation. As expected, the control peptide (pseudosubstrate) did not penetrate cells, affect cell proliferation or survival. We also show that a neoplastic T-cell line which expresses higher levels of PKC is more resistant to chimeric peptide-mediated cell death than normal cells, corroborating a PKC role in apoptosis resistance. This chimeric peptide could be useful for the specific modulation of the PKC signalling pathway in pathological conditions.     

DynBench3D,a Web-Resource to Dynamically Generate Benchmark Sets of Large Heteromeric Protein Complexes

Multi-protein machines are responsible for most cellular tasks, and many efforts have been invested in the systematic identification and characterization of thousands of these macromolecular assemblies. However, unfortunately, the (quasi) atomic details necessary to understand their function are available only for a tiny fraction of the known complexes. The computational biology community is developing strategies to integrate structural data of different nature, from electron microscopy to X-ray crystallography, to model large molecular machines, as it has been done for individual proteins and interactions with remarkable success. However, unlike for binary interactions, there is no reliable gold-standard set of three-dimensional (3D) complexes to benchmark the performance of these methodologies and detect their limitations. Here, we present a strategy to dynamically generate non-redundant sets of 3D heteromeric complexes with three or more components. By changing the values of sequence identity and component overlap between assemblies required to define complex redundancy, we can create sets of representative complexes with known 3D structure (i.e., target complexes). Using an identity threshold of 20% and imposing a fraction of component overlap of < 0.5, we identify 495 unique target complexes, which represent a real non-redundant set of heteromeric assemblies with known 3D structure. Moreover, for each target complex, we also identify a set of assemblies, of varying degrees of identity and component overlap, that can be readily used as input in a complex modeling exercise (i.e., template subcomplexes). We hope that resources like this will significantly help the development and progress assessment of novel methodologies, as docking benchmarks and blind prediction contests did. The interactive resource is accessible at https://DynBench3D.irbbarcelona.org.     

A Novel 3.5 kDa Protein Component of Cyanobacterial Photosystem I Complexes

A novel protein component of 3.5 kDa was detected in photosystemI complexes prepared from several cyanobacteria, viz. Synechococcusvulcanus, Synechococcus elongotus BP-1, Synechococcus sp. FCC7002 and Synechocystis sp. FCC 6803. The complete amino acidsequence of this component was determined by direct proteinsequencing. The sequences of the 3.5 kDa proteins from thesefour organisms were highly homologous to each other, featuringa hydrophobic domain in the middle. The cyanobacterial consensussequence exhibits significant homology to the presumed productof ORF32 in the chloroplast DNA of liverwort (Marchantia polymorpha),but no homologous ORF is present in the chloroplast DNA of tobaccoor rice. Since this protein appears to interact strongly withthe PS I reaction center complex, it may play some role in thefunction and maintenance of the structure of PS I. (Received May 25, 1992; Accepted August 18, 1992)     

Protein Complexes in Bacteria

Large-scale analyses of protein complexes have recently become available for Escherichia coli and Mycoplasma pneumoniae, yielding 443 and 116 heteromultimeric soluble protein complexes, respectively. We have coupled the results of these mass spectrometry-characterized protein complexes with the 285 “gold standard” protein complexes identified by EcoCyc. A comparison with databases of gene orthology, conservation, and essentiality identified proteins conserved or lost in complexes of other species. For instance, of 285 “gold standard” protein complexes in E. coli, less than 10% are fully conserved among a set of 7 distantly-related bacterial “model” species. Complex conservation follows one of three models: well-conserved complexes, complexes with a conserved core, and complexes with partial conservation but no conserved core. Expanding the comparison to 894 distinct bacterial genomes illustrates fractional conservation and the limits of co-conservation among components of protein complexes: just 14 out of 285 model protein complexes are perfectly conserved across 95% of the genomes used, yet we predict more than 180 may be partially conserved across at least half of the genomes. No clear relationship between gene essentiality and protein complex conservation is observed, as even poorly conserved complexes contain a significant number of essential proteins. Finally, we identify 183 complexes containing well-conserved components and uncharacterized proteins which will be interesting targets for future experimental studies.     

Isozyme Phenotypes for the Identification of Meloidogyne Species

Extensive studies during the last 20 years have demonstrated that enzyme phenotypes, especially those of esterases, are species-specific for Meloidogyne and can be used as reliable taxonomic characters for identification of most major and several minor species of this genus. Recent progress in electrophoretic procedures and advanced computer technology have made available automated electrophoretic apparati that can process very thin polyacrylamide slab gels on which the phenotypes of two or more enzymes can be revealed from the protein extract of a single Meloidogyne female. Presently, such apparati facilitate objective species identification. They also are convenient for performing routine field surveys to determine the relative distribution of major Meloidogyne species, conducting population dynamics studies in the field and in microplots, and testing the purity of greenhouse cultures.     

Subunit Exchange in Protein Complexes

Over the past 50?years, protein complexes have been studied with techniques such as X-ray crystallography and electron microscopy, generating images which although detailed are static and homogeneous. More recently, limited application of in vivo fluorescence and other techniques has revealed that many complexes previously thought stable and compositionally uniform are dynamically variable, continually exchanging components with a freely circulating pool of “spares.” Here, we consider the purpose and prevalence of protein exchange, first reviewing the ongoing story of exchange in the bacterial flagella motor, before surveying reports of exchange in complexes across all domains of life, together highlighting great diversity in timescales and functions. Finally, we put this in the context of high-throughput proteomic studies which hint that exchange might be the norm, rather than an exception.     

Use of Enzyme Phenotypes for Identification of Meloidogyne Species

Enzyme phenotypes were obtained for 291 populations from 16 species of Meloidogyne originating from 65 countries. Soluble proteins from macerates of individual egg-laying females were separated by electrophoresis in 0.7-mm-thick polyacrylamide gels. Enzymes investigated were nonspecific esterases, malate dehydrogenase, superoxide dismutase, and glutamate-oxaloacetate transaminase. Esterases were polymorphic and most useful in identification of major species. About 94% of the populations of M. hapla, 98% of M. incognita, and 100% of M. javanica could be identified to species on the basis of esterase phenotypes alone. About 84% of the populations of M. arenaria exhibited three distinct phenotypes. Two of them were highly species specific (accuracy of identification 98-100%). The third, and least prevalent, phenotype occurred also in two other species. Another 12 less common Meloidogyne species, of which only one or a few populations of each were studied, exhibited a variety of esterase phenotypes, some of which may prove to be species specific. Superoxide dismutase phenotypes similarly were helpful in the characterization of certain species; however, the same phenotype was often observed in more than one species. The remaining two enzymes, with few exceptions, proved to be less useful for identification of Meloidogyne species. Multienzyme phenotypes represented by two or more enzymes often offered biochemical profiles more valuable for definitive characterization of Meloidogyne species than single enzymes.     

Characterization of Virulence-Related Phenotypes in Candida Species of the CUG Clade

Candida species cause a variety of mucosal and invasive infections and are, collectively, the most important human fungal pathogens in the developed world. The majority of these infections result from a few related species within the “CUG clade,” so named because they use a nonstandard translation for that codon. Some members of the CUG clade, such as Candida albicans, present significant clinical problems, whereas others, such as Candida (Meyerozyma) guilliermondii, are uncommon in patients. The differences in incidence rates are imperfectly correlated with virulence in animal models of infection, but comparative analyses that might provide an explanation for why some species are effective pathogens and others are not have been rare or incomplete. To better understand the phenotypic basis for these differences, we characterized eight CUG clade species—C. albicans, C. dubliniensis, C. tropicalis, C. parapsilosis, Clavispora lusitaniae, M. guilliermondii, Debaryomyces hansenii, and Lodderomyces elongisporus—for host-relevant phenotypes, including nutrient utilization, stress tolerance, morphogenesis, interactions with phagocytes, and biofilm formation. Two species deviated from expectations based on animal studies and human incidence. C. dubliniensis was quite robust, grouping in nearly all assays with the most virulent species, C. albicans and C. tropicalis, whereas C. parapsilosis was substantially less fit than might be expected from its clinical importance. These findings confirm the utility of in vitro measures of virulence and provide insight into the evolution of virulence in the CUG clade.     

Lipid-Membrane Affinity of Chimeric Metal-binding Green Fluorescent Protein

The Green Fluorescent Protein (GFP) is a useful marker to trace the expression of cellular proteins. However, little is known about changes in protein interaction properties after fusion to GFP. In this study, we present evidence for a binding affinity of chimeric cadmium-binding green fluorescent proteins to lipid membrane. This affinity has been observed in both cellular membranes and artificial lipid monolayers and bilayers. At the cellular level, the presence of Cd-binding peptide promoted the association of the chimeric GFP onto the lipid membrane, which declined the fluorescence emission of the engineered cells. Binding affinity to lipid membranes was further investigated using artificial lipid bilayers and monolayers. Small amounts of the chimeric GFP were found to incorporate into the lipid vesicles due to the high surface pressure of bilayer lipids. At low interfacial pressure of the lipid monolayer, incorporation of the chimeric Cd-binding GFP onto the lipid monolayer was revealed. From the measured lipid isotherms, we conclude that Cd-binding GFP mediates an increase in membrane fluidity and an expansion of the surface area of the lipid film. This evidence was strongly supported by epifluorescence microscopy, showing that the chimeric Cd-binding GFP preferentially binds to fluid-phase areas and defect parts of the lipid monolayer. All these findings demonstrate the hydrophobicity of the GFP constructs is mainly influenced by the fusion partner. Thus, the example of a metal-binding unit used here shines new light on the biophysical properties of GFP constructs.This revised version was published online in June 2005 with a corrected cover date.     

Protein Engineering of Wzc To Generate New Emulsan Analogs

Acinetobacter venetianus Rag1 produces an extracellular, polymeric lipoheteropolysaccharide termed apoemulsan. This polymer is putatively produced via a Wzy-dependent pathway. According to this model, the length of the polymer is regulated by polysaccharide-copolymerase (PCP) protein. A highly conserved proline and glycine motif was identified in all members of the PCP family of proteins and is involved in regulation of polymer chain length. In order to control the structure of apoemulsan, defined point mutations in the proline-glycine-rich region of the apoemulsan PCP protein (Wzc) were introduced. Modified wzc variants were introduced into the Rag1 genome via homologous recombination. Stable chromosomal mutants were confirmed by Southern blot analysis. The molecular weight of the polymer was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Five of the eight point mutants produced polymers having molecular weights higher than the molecular weight of the polymer produced by the wild type. Moreover, four of these five polymers had modified biological properties. Replacement of arginine by leucine (R418L) resulted in the most significant change in the molecular weight of the polymer. The R418L mutant was the most hydrophilic mutant, exhibiting decreased adherence to polystyrene, and inhibited biofilm formation. The results described in this report show the functional effect of Wzc modification on the molecular weight of a high-molecular-weight polysaccharide. Moreover, in the present study we developed a genetic system to control polymerization of apoemulsan. The use of selective exogenous fatty acid feeding strategies, as well as genetic manipulation of sugar backbone chain length, is a promising new approach for bioengineering emulsan analogs.     

Protein Connectivity in Chemotaxis Receptor Complexes

The chemotaxis sensory system allows bacteria such as Escherichia coli to swim towards nutrients and away from repellents. The underlying pathway is remarkably sensitive in detecting chemical gradients over a wide range of ambient concentrations. Interactions among receptors, which are predominantly clustered at the cell poles, are crucial to this sensitivity. Although it has been suggested that the kinase CheA and the adapter protein CheW are integral for receptor connectivity, the exact coupling mechanism remains unclear. Here, we present a statistical-mechanics approach to model the receptor linkage mechanism itself, building on nanodisc and electron cryotomography experiments. Specifically, we investigate how the sensing behavior of mixed receptor clusters is affected by variations in the expression levels of CheA and CheW at a constant receptor density in the membrane. Our model compares favorably with dose-response curves from in vivo Förster resonance energy transfer (FRET) measurements, demonstrating that the receptor-methylation level has only minor effects on receptor cooperativity. Importantly, our model provides an explanation for the non-intuitive conclusion that the receptor cooperativity decreases with increasing levels of CheA, a core signaling protein associated with the receptors, whereas the receptor cooperativity increases with increasing levels of CheW, a key adapter protein. Finally, we propose an evolutionary advantage as explanation for the recently suggested CheW-only linker structures.     

Novel Nuclear Protein Complexes of Dystrophin 71 Isoforms in Rat Cultured Hippocampal GABAergic and Glutamatergic Neurons

The precise functional role of the dystrophin 71 in neurons is still elusive. Previously, we reported that dystrophin 71d and dystrophin 71f are present in nuclei from cultured neurons. In the present work, we performed a detailed analysis of the intranuclear distribution of dystrophin 71 isoforms (Dp71d and Dp71f), during the temporal course of 7-day postnatal rats hippocampal neurons culture for 1h, 2, 4, 10, 15 and 21 days in vitro (DIV). By immunofluorescence assays, we detected the highest level of nuclear expression of both dystrophin Dp71 isoforms at 10 DIV, during the temporal course of primary culture. Dp71d and Dp71f were detected mainly in bipolar GABAergic (≥60%) and multipolar Glutamatergic (≤40%) neurons, respectively. We also characterized the existence of two nuclear dystrophin-associated protein complexes (DAPC): dystrophin 71d or dystrophin 71f bound to β-dystroglycan, α1-, β-, α2-dystrobrevins, α-syntrophin, and syntrophin-associated protein nNOS (Dp71d-DAPC or Dp71f-DAPC, respectively), in the hippocampal neurons. Furthermore, both complexes were localized in interchromatin granule cluster structures (nuclear speckles) of neuronal nucleoskeleton preparations. The present study evinces that each Dp71’s complexes differ slightly in dystrobrevins composition. The results demonstrated that Dp71d-DAPC was mainly localized in bipolar GABAergic and Dp71f-DAPC in multipolar Glutamatergic hippocampal neurons. Taken together, our results show that dystrophin 71d, dystrophin 71f and DAP integrate protein complexes, and both complexes were associated to nuclear speckles structures.     

OLIG2 Drives Abnormal Neurodevelopmental Phenotypes in Human iPSC-Based Organoid and Chimeric Mouse Models of Down Syndrome

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