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1.
PLoS One ; 9(11): e111917, 2014.
Article in English | MEDLINE | ID: mdl-25369234

ABSTRACT

The extracellular membranes of the inner ear are essential constituents to maintain sensory functions, the cupula for sensing torsional movements of the head, the otoconial membrane for sensing linear movements and accelerations like gravity, and the tectorial membrane in the cochlea for hearing. So far a number of structural proteins have been described, but for the gelatinous cupula precise data are missing. Here, we describe for the first time a major proteinogenic component of the cupula structure with an apparent molecular mass of 45 kDa from salmon. Analyses of respective peptides revealed highly conserved amino-acid sequences with identity to zona pellucida-like domain proteins. Immunohistochemistry studies localized the protein in the ampulla of the inner ear from salmon and according to its anatomical appearance we identified this glycoprotein as Cupulin. Future research on structure and function of zona pellucida-like domain proteins will enhance our knowledge of inner ear diseases, like sudden loss of vestibular function and other disturbances.


Subject(s)
Avian Proteins/metabolism , Ear, Inner/metabolism , Fish Proteins/metabolism , Salmon/metabolism , Amino Acid Sequence , Animals , Avian Proteins/chemistry , Chickens , Fish Proteins/chemistry , Guinea Pigs , Membrane Proteins/chemistry , Molecular Sequence Data , Protein Structure, Tertiary , Rabbits , Sequence Homology, Amino Acid
2.
J Biol Chem ; 289(46): 31805-31817, 2014 Nov 14.
Article in English | MEDLINE | ID: mdl-25278022

ABSTRACT

SHH (Sonic Hedgehog)-GLI signaling plays an important role during embryogenesis and in tumorigenesis. The survival and growth of several types of cancer depend on autonomously activated SHH-GLI signaling. A protein complex containing the ubiquitin ligase MID1 and protein phosphatase 2A regulates the nuclear localization and transcriptional activity of GLI3, a transcriptional effector molecule of SHH, in cancer cell lines with autonomously activated SHH signaling. However, the exact molecular mechanisms that mediate the interaction between MID1 and GLI3 remained unknown. Here, we show that MID1 catalyzes the ubiquitination and proteasomal cleavage of the GLI3 regulator Fu. Our data suggest that Fu ubiquitination and cleavage is one of the key elements connecting the MID1-PP2A protein complex with GLI3 activity control.


Subject(s)
Kruppel-Like Transcription Factors/metabolism , Microtubule Proteins/metabolism , Nerve Tissue Proteins/metabolism , Nuclear Proteins/metabolism , Protein Serine-Threonine Kinases/metabolism , Transcription Factors/metabolism , Ubiquitin-Protein Ligases/chemistry , Catalysis , Cell Line, Tumor , Cell Nucleus/metabolism , DNA Primers , Gene Expression Regulation, Neoplastic , HeLa Cells , Hedgehog Proteins/metabolism , Humans , Lysine/chemistry , Proteasome Endopeptidase Complex/metabolism , Signal Transduction , Ubiquitin/chemistry , Ubiquitination , Zinc Finger Protein Gli3
3.
Protein Eng Des Sel ; 24(1-2): 79-87, 2011 Jan.
Article in English | MEDLINE | ID: mdl-21075772

ABSTRACT

The hexokinase isoenzyme 2 of Saccharomyces cerevisiae (ScHxk2) represents an archetype of a two-domain protein with the active site located in a cleft between the two domains. Binding of the substrate glucose results in a rigid body movement of the two domains leading to a cleft closure of the active site. Both domains of this enzyme are composed of discontinuous peptide sequences. This structural feature is reflected in the stability and folding of the ScHxk2 protein. Structural transitions induced by urea treatment resulted in the population of a thermodynamically stable folding intermediate, which, however, does not correspond to a molecule with one domain folded and the other unfolded. As demonstrated by different spectroscopic techniques, both domains are structurally affected by the partial denaturation. The intermediate possesses only 40% of the native secondary structural content and a substantial increase in the Stokes radius as judged by circular dichroism and dynamic light scattering analyses. One-dimensional ¹H NMR data prove that all tryptophan residues are in a non-native environment in the intermediate, indicating substantial changes in the tertiary structure. Still, the intermediate possesses quite a high stability for a transition intermediate of about ΔG = -22 kJ mol⁻¹.


Subject(s)
Hexokinase/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae/enzymology , Models, Molecular , Nuclear Magnetic Resonance, Biomolecular , Protein Denaturation , Protein Folding , Protein Structure, Tertiary
4.
J Biol Chem ; 285(52): 41019-33, 2010 Dec 24.
Article in English | MEDLINE | ID: mdl-20943665

ABSTRACT

Crystal structures of the unique hexokinase KlHxk1 of the yeast Kluyveromyces lactis were determined using eight independent crystal forms. In five crystal forms, a symmetrical ring-shaped homodimer was observed, corresponding to the physiological dimer existing in solution as shown by small-angle x-ray scattering. The dimer has a head-to-tail arrangement such that the small domain of one subunit interacts with the large domain of the other subunit. Dimer formation requires favorable interactions of the 15 N-terminal amino acids that are part of the large domain with amino acids of the small domain of the opposite subunit, respectively. The head-to-tail arrangement involving both domains of the two KlHxk1 subunits is appropriate to explain the reduced activity of the homodimer as compared with the monomeric enzyme and the influence of substrates and products on dimer formation and dissociation. In particular, the structure of the symmetrical KlHxk1 dimer serves to explain why phosphorylation of conserved residue Ser-15 may cause electrostatic repulsions with nearby negatively charged residues of the adjacent subunit, thereby inducing a dissociation of the homologous dimeric hexokinases KlHxk1 and ScHxk2. Two complex structures of KlHxk1 with bound glucose provide a molecular model of substrate binding to the open conformation and the subsequent classical domain closure motion of yeast hexokinases. The entirety of the novel data extends the current concept of glucose signaling in yeast and complements the induced-fit model by integrating the events of N-terminal phosphorylation and dissociation of homodimeric yeast hexokinases.


Subject(s)
Fungal Proteins/chemistry , Hexokinase/chemistry , Kluyveromyces/enzymology , Models, Molecular , Protein Multimerization/physiology , Crystallography, X-Ray , Fungal Proteins/metabolism , Glucose/chemistry , Glucose/metabolism , Hexokinase/metabolism , Phosphorylation/physiology , Protein Structure, Quaternary , Protein Structure, Tertiary
5.
FASEB J ; 24(10): 4000-19, 2010 Oct.
Article in English | MEDLINE | ID: mdl-20570965

ABSTRACT

Many proteins mature within the secretory pathway by the acquisition of glycans. Failure to maintain the proper distribution of the glycosylation machinery might lead to disease. High expression levels of the ubiquitous Golgi protein estrogen receptor-binding fragment-associated gene 9 (EBAG9) in human tumors correlate with poor clinical prognosis, and EBAG9 overexpression in epithelial cell lines induces truncated glycans, typical of many carcinomas. Here, we addressed the pathogenetic link between EBAG9 expression and the alteration of the cellular glycome. We applied confocal microscopy, live imaging, pulse-chase labeling in conjunction with immunoprecipitation, and enzymatic activity assays in a variety of EBAG9-overexpressing or depleted epithelial tumor cell lines. EBAG9 shuttles between the ER-Golgi intermediate compartment and the cis-Golgi, and we demonstrate association of EBAG9 with coat protein complex I (COPI)-coated transport vesicles. EBAG9 overexpression imposes delay of endoplasmic reticulum-to-Golgi transport and mislocalizes components of the ER quality control and glycosylation machinery. Conversely, EBAG9 down-regulation accelerates glycoprotein transport through the Golgi and enhances mannosidase activity. Thus, EBAG9 acts as a negative regulator of a COPI-dependent ER-to-Golgi transport pathway in epithelial cells and represents a novel pathogenetic principle in which interference with intracellular membrane trafficking results in the emergence of a tumor-associated glycome.


Subject(s)
Antigens, Neoplasm/physiology , Coat Protein Complex I/physiology , Glycoproteins/metabolism , Blotting, Western , Cell Line, Tumor , Fluorescent Antibody Technique , Humans
6.
FEMS Yeast Res ; 8(6): 858-69, 2008 Sep.
Article in English | MEDLINE | ID: mdl-18637841

ABSTRACT

The proteolytic potential of the pathogenic fungus Candida albicans was evaluated by the identification and functional characterization of a peptidolytic enzyme isolated from the cell wall of the microorganism. Determination of basic structural and kinetic data identified a neutral arginine/alanine/leucine-specific metallo-aminopeptidase of unknown function termed CaApe2, which is encoded by ORF CaO19.5197 (GenBank RefSeq XM_705313). Mass spectrometric tryptic peptide analysis and N-terminal protein sequencing revealed serine-88 to represent the N-terminus of CaApe2. Taking into account the results of DNA and protein sequence analysis including inspection of the genomic region upstream of ORF CaO19.5197, the gene CaAPE2 is likely to consist of two exons linked by a phase-2 intron with exons 1 and 2 encoding a signal peptide and the amino acids 88-954 of ORF CaO19.5197, respectively. The isolated CaApe2 protein shares an equally high similarity with the gene products ScAap1 and ScApe2, suggesting duplication of a phylogenetically ancient precursor gene in Saccharomyces cerevisiae. The observed failure to cleave human type-I and type-IV collagen in vitro challenges a direct role that secreted CaApe2 might play in the degradation of extracellular matrix components during host colonization, but does not exclude per se a contribution of the aminopeptidase to the pathogenicity of C. albicans.


Subject(s)
Aminopeptidases , Candida albicans/enzymology , Cell Wall/metabolism , Alanine/chemistry , Amino Acid Sequence , Aminopeptidases/chemistry , Aminopeptidases/genetics , Aminopeptidases/isolation & purification , Aminopeptidases/metabolism , Arginine/chemistry , Base Sequence , Candida albicans/genetics , Candida albicans/growth & development , Fungal Proteins/chemistry , Fungal Proteins/genetics , Fungal Proteins/immunology , Fungal Proteins/metabolism , Hydrogen-Ion Concentration , Kinetics , Leucyl Aminopeptidase/chemistry , Leucyl Aminopeptidase/genetics , Leucyl Aminopeptidase/isolation & purification , Leucyl Aminopeptidase/metabolism , Molecular Sequence Data , Substrate Specificity , Temperature
7.
PLoS One ; 3(7): e2780, 2008 Jul 23.
Article in English | MEDLINE | ID: mdl-18648668

ABSTRACT

Eph receptors are the largest family of receptor tyrosine kinases. Together with their ligands, the ephrins, they fulfill multiple biological functions. Aberrant expression of Ephs/ephrins leading to increased Eph receptor to ephrin ligand ratios is a critical factor in tumorigenesis, indicating that tight regulation of Eph and ephrin expression is essential for normal cell behavior. The 3'-untranslated regions (3'UTRs) of transcripts play an important yet widely underappreciated role in the control of protein expression. Based on the assumption that paralogues of large gene families might exhibit a conserved organization of regulatory elements in their 3'UTRs we applied a novel bioinformatics/molecular biology approach to the 3'UTR sequences of Eph/ephrin transcripts. We identified clusters of motifs consisting of cytoplasmic polyadenylation elements (CPEs), AU-rich elements (AREs) and HuR binding sites. These clusters bind multiple RNA-stabilizing and destabilizing factors, including HuR. Surprisingly, despite its widely accepted role as an mRNA-stabilizing protein, we further show that binding of HuR to these clusters actually destabilizes Eph/ephrin transcripts in tumor cell lines. Consequently, knockdown of HuR greatly modulates expression of multiple Ephs/ephrins at both the mRNA and protein levels. Together our studies suggest that overexpression of HuR as found in many progressive tumors could be causative for disarranged Eph receptor to ephrin ligand ratios leading to a higher degree of tissue invasiveness.


Subject(s)
Antigens, Surface/metabolism , Ephrin-A1/metabolism , Ephrin-B2/metabolism , Gene Expression Regulation, Neoplastic , RNA-Binding Proteins/metabolism , Receptors, Eph Family/biosynthesis , 3' Untranslated Regions , Amino Acid Motifs , Animals , Base Sequence , Cell Line, Tumor , Cytoplasm/metabolism , ELAV Proteins , ELAV-Like Protein 1 , Humans , Mice , Molecular Sequence Data , Sequence Homology, Nucleic Acid
8.
J Neurochem ; 106(1): 372-83, 2008 Jul.
Article in English | MEDLINE | ID: mdl-18419770

ABSTRACT

OPA1, a nuclear encoded mitochondrial protein causing autosomal dominant optic atrophy, is a key player in mitochondrial fusion and cristae morphology regulation. In the present study, we have compared the OPA1 transcription and translation products of different mouse tissues. Unlike in humans, we found only two exons (4b and 5b) to be involved in alternative splicing. The relative abundance of the resulting four different splice variants is tissue-dependent. Proteolytic cleavage by mitochondrial processing peptidase generates two long forms, isoforms 1 and 7, which lead to three short forms representing the end products after further proteolytic processing. In contrast, isoforms 5 and 8 are directly processed into their corresponding short forms. Short form 1 molecules form 184 kDa dimers, whereas all other isoforms contribute to 285 kDa complexes. Coiled-coil domains of the OPA1 protein specifically homo-associate and may be involved in the formation of these complexes. Furthermore, the region encoded by exon 5b inhibits the self-association of coiled-coil domain-I. Finally, our data pinpoint isoform 1 as the, by far, most abundant isoform in the nervous tissue. We postulate that manipulation of isoform 1 protein levels in relation to the other isoforms induces changes in the mitochondrial network in the cell and therefore, mutations affecting the level of functional isoform 1 could lead to devastating effects on retinal ganglion cells.


Subject(s)
Alternative Splicing/genetics , GTP Phosphohydrolases/genetics , Mitochondria/genetics , Mitochondrial Proteins/genetics , Optic Atrophy, Autosomal Dominant/genetics , Amino Acid Sequence/genetics , Animals , Base Sequence/genetics , Brain/metabolism , Exons/genetics , GTP Phosphohydrolases/isolation & purification , GTP Phosphohydrolases/metabolism , Kidney/metabolism , Liver/metabolism , Mice , Mice, Inbred C57BL , Mitochondria/metabolism , Mitochondria/ultrastructure , Mitochondrial Proteins/isolation & purification , Mitochondrial Proteins/metabolism , Molecular Sequence Data , Myocardium/metabolism , Optic Atrophy, Autosomal Dominant/metabolism , Protein Isoforms/genetics , Protein Isoforms/isolation & purification , Protein Isoforms/metabolism , Retinal Ganglion Cells/metabolism , Retinal Ganglion Cells/pathology , Subcellular Fractions
9.
Hum Genet ; 123(2): 163-76, 2008 Mar.
Article in English | MEDLINE | ID: mdl-18172692

ABSTRACT

Opitz BBB/G syndrome (OS) is a heterogenous malformation syndrome mainly characterised by hypertelorism and hypospadias. In addition, patients may present with several other defects of the ventral midline such as cleft lip and palate and congenital heart defects. The syndrome-causing gene encodes the X-linked E3 ubiquitin ligase MID1 that mediates ubiquitin-specific modification and degradation of the catalytic subunit of the translation regulator protein phosphatase 2A (PP2A). Here, we show that the MID1 protein also associates with elongation factor 1alpha (EF-1alpha) and several other proteins involved in mRNA transport and translation, including RACK1, Annexin A2, Nucleophosmin and proteins of the small ribosomal subunits. Mutant MID1 proteins as found in OS patients lose the ability to interact with EF-1alpha. The composition of the MID1 protein complex was determined by several independent methods: (1) yeast two-hybrid screening and (2) immunofluorescence, (3) a biochemical approach involving affinity purification of the complex, (4) co-fractionation in a microtubule assembly assay and (5) immunoprecipitation. Moreover, we show that the cytoskeleton-bound MID1/translation factor complex specifically associates with G- and U-rich RNAs and incorporates MID1 mRNA, thus forming a microtubule-associated ribonucleoprotein (RNP) complex. Our data suggest a novel function of the OS gene product in directing translational control to the cytoskeleton. The dysfunction of this mechanism would lead to malfunction of microtubule-associated protein translation and to the development of OS.


Subject(s)
Microtubule Proteins/genetics , Microtubules/metabolism , Nuclear Proteins/genetics , Peptide Elongation Factor 1/metabolism , RNA/metabolism , Ribonucleoproteins/metabolism , Transcription Factors/genetics , Annexin A2/genetics , Annexin A2/metabolism , Base Sequence , Chromatography, Affinity , Fluorescent Antibody Technique , GTP-Binding Proteins/genetics , GTP-Binding Proteins/metabolism , Genetic Diseases, X-Linked/genetics , HeLa Cells , Humans , Immunoprecipitation , In Situ Hybridization , Microtubule Proteins/metabolism , Molecular Sequence Data , Neoplasm Proteins/genetics , Neoplasm Proteins/metabolism , Nuclear Proteins/metabolism , Nucleophosmin , Peptide Elongation Factor 1/genetics , RNA, Small Interfering/pharmacology , Receptors for Activated C Kinase , Receptors, Cell Surface/genetics , Receptors, Cell Surface/metabolism , Ribonucleoproteins/genetics , Sequence Homology, Nucleic Acid , Transcription Factors/metabolism , Two-Hybrid System Techniques , Ubiquitin-Protein Ligases
10.
FEMS Yeast Res ; 7(5): 683-92, 2007 Aug.
Article in English | MEDLINE | ID: mdl-17573926

ABSTRACT

Recent data suggest that hexokinase KlHxk1 (Rag5) represents the only glucose-phosphorylating enzyme of Kluyveromyces lactis, which also is required for glucose signalling. Long-term growth studies of a K. lactis rag5 mutant, however, reveal slow growth on glucose, but no growth on fructose. Isolation of the permissive glucose-phosphorylating enzyme, mass spectrometric tryptic peptide analysis and determination of basic kinetic data identify a novel glucokinase (KlGlk1) encoded by ORF KLLA0C01,155g. In accordance with the growth characteristics of the rag5 mutant, KlGlk1 phosphorylates glucose, but fails to act on fructose as a sugar substrate. Multiple sequence alignment indicates the presence of at least one glucokinase gene in all sequenced yeast genomes.


Subject(s)
Gene Expression Regulation, Fungal , Glucokinase , Kluyveromyces/enzymology , Amino Acid Sequence , Fructose/metabolism , Fungal Proteins/chemistry , Fungal Proteins/genetics , Fungal Proteins/isolation & purification , Fungal Proteins/metabolism , Glucokinase/chemistry , Glucokinase/genetics , Glucokinase/isolation & purification , Glucokinase/metabolism , Glucose/metabolism , Humans , Kluyveromyces/genetics , Kluyveromyces/growth & development , Molecular Sequence Data , Phosphorylation , Phylogeny , Sequence Alignment , Substrate Specificity
11.
Biophys Chem ; 125(1): 159-65, 2007 Jan.
Article in English | MEDLINE | ID: mdl-16916573

ABSTRACT

The mitochondrial steroid hydroxylase system of vertebrates utilizes adrenodoxin (Adx), a small iron-sulfur cluster protein of about 14 kDa as an electron carrier between a reductase and cytochrome P450. Although the crystal structure of this protein has been elucidated, the solution structure of Adx was discussed contrary in the literature [I.A. Pikuleva, K. Tesh, M.R. Waterman, Y. Kim, The tertiary structure of full-length bovine adrenodoxin suggests functional dimers, Arch. Biochem. Biophys. 373 (2000) 44-55; D. Beilke, R. Weiss, F. Löhr, P. Pristovsek, F. Hannemann, R. Bernhardt, H. Rüterjans, A new electron mechanism in mitochondrial steroid hydroxylase systems based on structural changes upon the reduction of adrenodoxin, Biochemistry 41 (2002) 7969-7978]. Therefore, it was necessary to study the self-association of this protein by using analytical ultracentrifugation over a larger concentration range. As could be demonstrated in sedimentation velocity experiments, as well as sedimentation equilibrium runs with explicit consideration of thermodynamic non-ideality, the full-length protein (residues 1-128) in the oxidized state resulted in a monomer-dimer equilibrium (K(a) approximately 3 x 10(2) M(-1)). For truncated Adx (1-108), as well as the reduced Adx, the association behavior was strongly reduced. The consequences of this behavior are discussed with respect to the physiological meaning for the Adx system.


Subject(s)
Adrenodoxin/chemistry , Protein Structure, Quaternary , Oxidation-Reduction , Thermodynamics , Ultracentrifugation/methods
12.
Mol Cell Proteomics ; 5(2): 234-44, 2006 Feb.
Article in English | MEDLINE | ID: mdl-16275660

ABSTRACT

Proteins mediate their biological function through interactions with other proteins. Therefore, the systematic identification and characterization of protein-protein interactions have become a powerful proteomic strategy to understand protein function and comprehensive cellular regulatory networks. For the screening of valosin-containing protein, carboxyl terminus of Hsp70-interacting protein (CHIP), and amphiphysin II interaction partners, we utilized a membrane-based array technology that allows the identification of human protein-protein interactions with crude bacterial cell extracts. Many novel interaction pairs such as valosin-containing protein/autocrine motility factor receptor, CHIP/caytaxin, or amphiphysin II/DLP4 were identified and subsequently confirmed by pull-down, two-hybrid and co-immunoprecipitation experiments. In addition, assays were performed to validate the interactions functionally. CHIP e.g. was found to efficiently polyubiquitinate caytaxin in vitro, suggesting that it might influence caytaxin degradation in vivo. Using peptide arrays, we also identified the binding motifs in the proteins DLP4, XRCC4, and fructose-1,6-bisphosphatase, which are crucial for the association with the Src homology 3 domain of amphiphysin II. Together these studies indicate that our human proteome array technology permits the identification of protein-protein interactions that are functionally involved in neurodegenerative disease processes, the degradation of protein substrates, and the transport of membrane vesicles.


Subject(s)
Cell Cycle Proteins/chemistry , Cell Cycle Proteins/metabolism , HSC70 Heat-Shock Proteins/metabolism , Nerve Tissue Proteins/metabolism , Protein Array Analysis , Protein Interaction Mapping , Proteome , Adenosine Triphosphatases , Amino Acid Sequence , Animals , COS Cells , Chlorocebus aethiops , Humans , Membranes, Artificial , Molecular Sequence Data , Protein Binding , Protein Structure, Tertiary , Valosin Containing Protein
13.
EMBO J ; 24(5): 875-84, 2005 Mar 09.
Article in English | MEDLINE | ID: mdl-15692564

ABSTRACT

BET3 is a component of TRAPP, a complex involved in the tethering of transport vesicles to the cis-Golgi membrane. The crystal structure of human BET3 has been determined to 1.55-A resolution. BET3 adopts an alpha/beta-plait fold and forms dimers in the crystal and in solution, which predetermines the architecture of TRAPP where subunits are present in equimolar stoichiometry. A hydrophobic pocket within BET3 buries a palmitate bound through a thioester linkage to cysteine 68. BET3 and yeast Bet3p are palmitoylated in recombinant yeast cells, the mutant proteins BET3 C68S and Bet3p C80S remain unmodified. Both BET3 and BET3 C68S are found in membrane and cytosolic fractions of these cells; in membrane extractions, they behave like tightly membrane-associated proteins. In a deletion strain, both Bet3p and Bet3p C80S rescue cell viability. Thus, palmitoylation is neither required for viability nor sufficient for membrane association of BET3, which may depend on protein-protein contacts within TRAPP or additional, yet unidentified modifications of BET3. A conformational change may facilitate palmitoyl extrusion from BET3 and allow the fatty acid chain to engage in intermolecular hydrophobic interactions.


Subject(s)
Membrane Proteins/chemistry , Vesicular Transport Proteins/chemistry , Amino Acid Sequence , Crystallography, X-Ray , Dimerization , Humans , In Vitro Techniques , Membrane Proteins/genetics , Membrane Proteins/metabolism , Models, Molecular , Molecular Sequence Data , Molecular Structure , Mutagenesis, Site-Directed , Palmitic Acid/chemistry , Protein Conformation , Protein Structure, Quaternary , Protein Subunits , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Sequence Homology, Amino Acid , Static Electricity , Vesicular Transport Proteins/genetics , Vesicular Transport Proteins/metabolism
14.
Proteomics ; 4(10): 2969-81, 2004 Oct.
Article in English | MEDLINE | ID: mdl-15378754

ABSTRACT

Chlamydophila pneumoniae is an obligate intracellular pathogen implicated in a variety of acute and chronic diseases. Long-term infections are associated with a persistent life stage, in which bacteria can stay for years. They are less accessible to antibiotic treatment but still prone to sustain an inflammatory response. Different in vitro models have been established to mimic and characterize chlamydial persistency. For C. pneumoniae and Chlamydia trachomatis, altered metabolic activities and changed antigenic profiles compared to acute infections have been reported. Most studies including transcriptome and proteome analyses describe persistency induced by IFNgamma treatment. Here, we use iron depletion of the infected cell culture that also leads into persistent infection. We describe differently regulated proteins found by subtractive proteome analysis comparing two early stages of infection with and without addition of the iron chelator deferoxamine-mesylate. While only one bacterial protein was up-regulated during iron deficiency up to 24 h post infection (p.i.), 11 were found to be up-regulated and eight to be down-regulated from 24-48 h p.i. Two down-regulated proteins could be identified by peptide mass fingerprinting as thioredoxin reductase and chromosome partitioning protein (ParB). The latter is involved in chromosome segregation. Thus, using a comparative approach we identified on a proteome level down-regulation of ParB in persistent chlamydial forms, which is in agreement with previous results describing changes in cell division and atypical altered morphology of persistent Chlamydiae.


Subject(s)
Chlamydophila Infections/metabolism , Chlamydophila pneumoniae/metabolism , Gene Expression Regulation, Bacterial , Genes, Bacterial , Iron Deficiencies , Proteome , Amino Acid Sequence , Antigens, Bacterial , Autoradiography , Bacterial Physiological Phenomena , Cell Division , Cell Line , Chlamydophila Infections/genetics , Down-Regulation , Electrophoresis, Gel, Two-Dimensional , Epithelium/microbiology , Fluorescent Dyes/pharmacology , Humans , Interferon-gamma/metabolism , Mass Spectrometry , Molecular Sequence Data , Spectrometry, Mass, Electrospray Ionization , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Time Factors , Trypsin/pharmacology , Up-Regulation
15.
Proteomics ; 4(10): 2954-60, 2004 Oct.
Article in English | MEDLINE | ID: mdl-15378760

ABSTRACT

ESAT-6 (the 6 kDa early secreted antigenic target) protein species in short-term culture filtrate of Mycobacterium tuberculosis were separated in a 4-5 narrow range pI gradient two-dimensional gel electrophoresis (2-DE). Eight ESAT-6 protein species were analyzed in detail by peptide mass fingerprinting matrix-assisted laser desorption/ionization-mass spectrometry as well as by electrospray ionization-tandem mass spectrometry. An N-terminal Thr acetylation was identified in four species and a C-terminal truncation was identified in two species. In 2-DE blot overlay assays, the recombinant 10 kDa culture filtrate protein (CFP10) discriminated N-terminal acetylated and nonacetylated ESAT-6 by differential interaction, whereas removal of the C-terminal 11 residues of ESAT-6 had no effects thereon. This example shows that the access to the protein species level can be a prerequisite to understand regulation of protein-protein interaction.


Subject(s)
Bacterial Proteins/chemistry , Mycobacterium tuberculosis/metabolism , Acetylation , Amino Acid Sequence , Antigens, Bacterial/chemistry , Electrophoresis, Gel, Two-Dimensional/methods , Humans , Hydrogen-Ion Concentration , Mass Spectrometry/methods , Molecular Sequence Data , Protein Binding , Protein Processing, Post-Translational , Protein Structure, Tertiary
16.
J Inorg Biochem ; 98(7): 1229-37, 2004 Jul.
Article in English | MEDLINE | ID: mdl-15219990

ABSTRACT

The single mitochondrial type I [2Fe-2S] ferredoxin of the fission yeast Schizosaccharomyces pombe is produced as the carboxy terminal part of the electron-transfer-protein 1 (etp1) and cleaved off during mitochondrial import [Biochemistry 41 (2002) 2311-2321]. The UV/Vis (UV-visible) spectrum of the purified recombinant ferredoxin domain (etp1(fd)) expressed in Escherichia coli is similar to those of bovine Adx in the oxidized as well as in the reduced state. EPR (electronic paramagnetic resonance) studies revealed a correctly incorporated iron-sulfur cluster of the axial type. The redox potential of this protein was determined to be -353 mV, which is considerably lower than that of adrenodoxin (Adx, -273 mV). Several lines of evidence indicate that the protein forms dimers under physiological and denaturating conditions. Interestingly, the fission yeast ferredoxin could be shown to be active as an electron carrier in heterologous redox systems. It is able to transfer electrons to horse heart cytochrome c and to bovine cytochromes P450(scc) (CYP11A1) and P450(11 beta) (CYP11B1), thereby receiving electrons from bovine NADPH-dependent Adx reductase. The kinetics of substrate conversion in the etp1(fd)-supported CYP11A1 and CYP11B1-dependent systems mediated was studied.


Subject(s)
Ferredoxins/chemistry , Mitochondria/enzymology , Schizosaccharomyces pombe Proteins/chemistry , Schizosaccharomyces/enzymology , Adrenodoxin , Amino Acid Sequence , Animals , Cattle , Cholesterol Side-Chain Cleavage Enzyme/chemistry , Ferredoxins/genetics , Molecular Sequence Data , Oxidation-Reduction , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Schizosaccharomyces/genetics , Schizosaccharomyces pombe Proteins/genetics , Sequence Homology, Amino Acid , Steroid 11-beta-Hydroxylase/chemistry
17.
Appl Environ Microbiol ; 70(2): 1040-50, 2004 Feb.
Article in English | MEDLINE | ID: mdl-14766587

ABSTRACT

We analyzed the biochemical composition of the magnetosome membrane (MM) in Magnetospirillum gryphiswaldense. Isolated magnetosomes were associated with phospholipids and fatty acids which were similar to phospholipids and fatty acids from other subcellular compartments (i.e., outer and cytoplasmic membranes) but were present in different proportions. The binding characteristics of MM-associated proteins were studied by selective solubilization and limited proteolysis. The MM-associated proteins were further analyzed by various proteomic approaches, including one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by Edman and mass spectrometric (electrospray ionization-mass spectrometry-mass spectrometry) sequencing, as well as capillary liquid chromatography-mass spectrometry-mass spectrometry of total tryptic digests of the MM. At least 18 proteins were found to constitute the magnetosome subproteome, and most of these proteins are novel for M. gryphiswaldense. Except for MM22 and Mms16, all bona fide MM proteins (MMPs) were encoded by open reading frames in the mamAB, mamDC, and mms6 clusters in the previously identified putative magnetosome island. Eight of the MMPs display homology to known families, and some of them occur in the MM in multiple homologues. Ten of the MMPs have no known homologues in nonmagnetic organisms and thus represent novel, magnetotactic bacterium-specific protein families. Several MMPs display repetitive or highly acidic sequence patterns, which are known from other biomineralizing systems and thus may have relevance for magnetite formation.


Subject(s)
Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Ferric Compounds , Intracellular Membranes/metabolism , Magnetospirillum/ultrastructure , Proteome , Amino Acid Sequence , Bacterial Proteins/chemistry , Ferric Compounds/chemistry , Ferric Compounds/metabolism , Intracellular Membranes/chemistry , Magnetospirillum/metabolism , Mass Spectrometry , Membrane Proteins/chemistry , Membrane Proteins/genetics , Membrane Proteins/metabolism , Molecular Sequence Data
18.
Mol Cell Proteomics ; 3(1): 43-55, 2004 Jan.
Article in English | MEDLINE | ID: mdl-14557597

ABSTRACT

In search of novel mechanisms leading to the development of antiestrogen-resistance in human breast tumors, we analyzed differences in the gene and protein expression pattern of the human breast carcinoma cell line T47D and its derivative T47D-r, which is resistant toward the pure antiestrogen ZM 182780 (Faslodex trade mark, fulvestrant). Affymetrix DNA chip hybridizations on the commercially available HuGeneFL and Hu95A arrays were carried out in parallel to the proteomics analysis where the total cellular protein content of T47D or T47D-r was separated on two-dimensional gels. Thirty-eight proteins were found to be reproducibly up- or down-regulated more than 2-fold in T47D-r versus T47D in the proteomics analysis. Comparison with differential mRNA analysis revealed that 19 of these were up- or down-regulated in parallel with the corresponding mRNA molecules, among which are the protease cathepsin D, the GTPases Rab11a and MxA, and the secreted protein hAG-2. For 11 proteins, the corresponding mRNA was not found to be differentially expressed, and for eight proteins an inverse regulation was found at the mRNA level. In summary, mRNA expression data, when combined with proteomic information, provide a more detailed picture of how breast cancer cells are altered in their antiestrogen-resistant compared with the antiestrogen-sensitive state.


Subject(s)
Breast Neoplasms/metabolism , Cell Line, Tumor/chemistry , Drug Resistance, Neoplasm , Estradiol/analogs & derivatives , Estrogen Receptor Modulators/metabolism , Gene Expression Profiling , Genome , Proteome/analysis , Breast Neoplasms/drug therapy , Breast Neoplasms/pathology , Cell Line, Tumor/drug effects , Cell Line, Tumor/physiology , Estradiol/metabolism , Estradiol/pharmacology , Estradiol/therapeutic use , Estrogen Antagonists/metabolism , Estrogen Antagonists/pharmacology , Estrogen Antagonists/therapeutic use , Estrogen Receptor Modulators/pharmacology , Estrogen Receptor Modulators/therapeutic use , Female , Fulvestrant , Gene Expression Regulation, Neoplastic , Humans , Oligonucleotide Array Sequence Analysis , Proteomics , RNA, Messenger/metabolism
19.
Electrophoresis ; 24(19-20): 3405-20, 2003 Oct.
Article in English | MEDLINE | ID: mdl-14595687

ABSTRACT

A comprehensive analysis of culture supernatant (CSN) proteins of Mycobacterium tuberculosis H37Rv was accomplished by combination of two-dimensional electrophoresis (2-DE), mass spectrometry, and N-terminal sequencing by Edman degradation. Analytical 2-DE gels resolved approximately 1250 protein spots from CSN of M. tuberculosis H37Rv, 381 of which were identified by mass spectrometry and/or Edman degradation. This study revealed 137 different proteins, 42 of which had previously been described as secreted. Comparative proteome analysis of CSN from virulent M. tuberculosis H37Rv and attenuated Mycobacterium bovis BCG Copenhagen identified 39 M. tuberculosis-specific spots containing 27 different proteins, representing candidate antigens for novel vaccines and diagnostics in tuberculosis. These included five proteins encoded by open reading frames absent from M. bovis BCG, e.g., early secretory antigen target (Esat6), as well as 22 novel differential proteins, such as acetyl-CoA C-acetyltransferase (Rv0243) and two putative Esat6-like proteins (Rv1198, Rv1793).


Subject(s)
Bacterial Proteins/analysis , Mycobacterium bovis/chemistry , Mycobacterium tuberculosis/chemistry , Proteomics/methods , Bacterial Proteins/metabolism , Culture Media, Conditioned/analysis , Electrophoresis, Gel, Two-Dimensional , Mass Spectrometry , Sequence Analysis, Protein
20.
J Protein Chem ; 22(3): 249-58, 2003 Apr.
Article in English | MEDLINE | ID: mdl-12962325

ABSTRACT

The 60S ribosomal proteins were isolated from ribosomes of human placenta and separated by reversed phase HPLC. The fractions obtained were subjected to trypsin and Glu-C digestion and analyzed by mass fingerprinting (MALDI-TOF), MS/MS (ESI), and Edman sequencing. Forty-six large subunit proteins were found, 22 of which showed masses in accordance with the SwissProt database (June 2002) masses (proteins L6, L7, L9, L13, L15, L17, L18, L21, L22, L24, L26, L27, L30, L32, L34, L35, L36, L37, L37A, L38, L39, L41). Eleven (proteins L7, L10A, L11, L12, L13A, L23, L23A, L27A, L28, L29, and P0) resulted in mass changes that are consistent with N-terminal loss of methionine, acetylation, internal methylation, or hydroxylation. A loss of methionine without acetylation was found for protein L8 and L17. For nine proteins (L3, L4, L5, L7A, L10, L14, L19, L31, and L40), the molecular masses could not be determined. Proteins P1 and protein L3-like were not identified by the methods applied.


Subject(s)
Protein Processing, Post-Translational , Ribosomal Proteins/chemistry , Ribosomal Proteins/metabolism , Amino Acid Sequence , Chromatography, High Pressure Liquid , Humans , Mass Spectrometry , Molecular Sequence Data , Molecular Weight , Ribosomal Proteins/isolation & purification , Sequence Analysis, Protein
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