Biomedical subjects

M Mann

Publications and source records attributed to M Mann.

At least 145 records · Page 8Linked to original sources

PubMed1997

Two functionally distinct domains generated by in vivo cleavage of Nup145p: a novel biogenesis pathway for nucleoporins.

Nup145p is an essential yeast nucleoporin involved in nuclear export of polyadenylated RNAs. We demonstrate here that Nup145p is cleaved in vivo to yield two functionally distinct domains: a carboxy-terminal domain (C-Nup145p) which is located at the nuclear pore complex (NPC) and assembles into the Nup84p complex, and a GLFG-containing amino-terminal domain (N-Nup145p) which is not part of this complex. Whereas the essential C-Nup145p accomplishes the functions required for efficient mRNA export and normal NPC distribution, N-Nup145p, which is homologous to the GLFG-containing nucleoporins Nup100p and Nup116p, is not necessary for cell growth. However, the N-Nup145p becomes essential in a nup188 mutant background. Strikingly, generation of a free N-domain is a prerequisite for complementation of this peculiar synthetic lethal mutant. These data suggest that N- and C-domains of Nup145p perform independent functions, and that the in vivo cleavage observed is of functional importance.

Amino Acid Sequence↗

PubMed1997

Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II.

Repressive chromatin structures need to be unravelled to allow DNA-binding proteins access to their target sequences. This de-repression constitutes an important point at which transcription and presumably other nuclear processes can be regulated. Energy-consuming enzyme complexes that facilitate the interaction of transcription factors with chromatin by modifying nucleosome structure are involved in this regulation. One such factor, nucleosome-remodelling factor (NURF), has been isolated from Drosophila embryo extracts. We have now identified a chromatin-accessibility complex (CHRAC) which uses energy to increase the general accessibility of DNA in chromatin. However, unlike other known chromatin remodelling factors, CHRAC can also function during chromatin assembly: it uses ATP to convert irregular chromatin into a regular array of nucleosomes with even spacing. CHRAC combines enzymes that modulate nucleosome structure and DNA topology. Using mass spectrometry, we identified two of the five CHRAC subunits as the ATPase ISWI, which is also part of NURF, and topoisomerase II. The presence of ISWI in different contexts suggests that chromatin remodelling machines have a modular nature and that ISWI has a central role in different chromatin remodelling reactions.

Adenosine Triphosphatases↗

PubMed1997

Activity of DNA ligase IV stimulated by complex formation with XRCC4 protein in mammalian cells.

Mutation of the XRCC4 gene in mammalian cells prevents the formation of the signal and coding joints in the V(D)J recombination reaction, which is necessary for production of a functional immunoglobulin gene, and renders the cells highly sensitive to ionizing radiation. However, XRCC4 shares no sequence homology with other proteins, nor does it have a biochemical activity to indicate what its function might be. Here we show that DNA ligase IV co-immunoprecipitates with XRCC4 and that these two proteins specifically interact with one another in a yeast two-hybrid system. Ligation of DNA double-strand breaks in a cell-free system by DNA ligase IV is increased fivefold by purified XRCC4 and seven- to eightfold when XRCC4 is co-expressed with DNA ligase IV. We conclude that the biological consequences of mutating XRCC4 are primarily due to the loss of its stimulatory effect on DNA ligase IV: the function of the XRCC4-DNA ligase IV complex may be to carry out the final steps of V(D)J recombination and joining of DNA ends.

Animals↗

PubMed1997

Rapid protein sequencing by tandem mass spectrometry and cDNA cloning of p20-CGGBP. A novel protein that binds to the unstable triplet repeat 5'-d(CGG)n-3' in the human FMR1 gene.

The autonomous expansion of the unstable 5'-d(CGG)n-3' repeat in the 5'-untranslated region of the human FMR1 gene leads to the fragile X syndrome, one of the most frequent causes of mental retardation in human males. We have recently described the isolation of a protein p20-CGGBP that binds sequence-specifically to the double-stranded trinucleotide repeat 5'-d(CGG)-3' (Deissler, H., Behn-Krappa, A., and Doerfler, W. (1996) J. Biol. Chem. 271, 4327-4334). We demonstrate now that the p20-CGGBP can also bind to an interrupted repeat sequence. Peptide sequence tags of p20-CGGBP obtained by nanoelectrospray mass spectrometry were screened against an expressed sequence tag data base, retrieving a clone that contained the full-length coding sequence for p20-CGGBP. A bacterially expressed fusion protein p20-CGGBP-6xHis exhibits a binding pattern to the double-stranded 5'-d(CGG)n-3' repeat similar to that of the authentic p20-CGGBP. This novel protein lacks any overall homology to other known proteins but carries a putative nuclear localization signal. The p20-CGGBP gene is conserved among mammals but shows no homology to non-vertebrate species. The gene encoding the sequence for the new protein has been mapped to human chromosome 3.

Amino Acid Sequence↗

PubMed1997

The complex containing actin-related proteins Arp2 and Arp3 is required for the motility and integrity of yeast actin patches.

BACKGROUND: Structural modeling and biochemical experiments in vitro have implicated a multi-protein complex containing two actin-related proteins, Arp2 and Arp3, as a potential actin-filament nucleation factor. This 'Arp2/3 complex' has been identified in Acanthamoeba and human cells and has been shown to localize to regions involved in actin-based motility, such as the leading edge of moving cells and the 'tail' of actin that forms behind the intracellular pathogen Listeria. The function of this complex in vivo has not been characterized, however, and the sequences of the non-actin-related subunits remain to be determined. RESULTS: An Arp3 homologue from the budding yeast Saccharomyces cerevisiae was found to localize to cortical actin patches, highly motile structures that concentrate at sites of polarized growth during the yeast cell cycle. A conditional arp3 mutant allele inhibited cortical actin motility at the restrictive temperature and eventually disrupted actin patches. Most Arp3 protein is found in a multi-protein complex; we purified this complex and determined the sequences of each of the protein subunits using a high-accuracy mass peptide-mapping technique. The proteins found in the complex are similar to those in the Acanthamoeba and human Arp2/3 complexes except that the yeast complex lacks a 40 kDa subunit, which is therefore not required for the structural integrity of the complex. CONCLUSIONS: The Arp2/3 protein complex is conserved from yeast to man, and in yeast the complex is required in vivo for the motility and integrity of cortical actin patches. We hypothesize that these patches may move by a Listeria-like mechanism driven by actin polymerization.

Actin-Related Protein 2↗

PubMed1997

SH2 signaling in a lower eukaryote: a STAT protein that regulates stalk cell differentiation in dictyostelium.

The TTGA-binding factor is a transcriptional regulator activated by DIF, the chlorinated hexaphenone that induces prestalk cell differentiation in Dictyostelium. The same activity also functions as a repressor, controlling stalk cell differentiation. We show that the TTGA-binding factor is a STAT protein. Like the metazoan STATs, it functions via the reciprocal interaction of a phosphotyrosine residue on one molecule with an SH2 domain on a dimerizing partner. Furthermore, it will bind specifically to a mammalian interferon-stimulated response element. In Saccharomyces cerevisiae, where the entire genomic sequence is known, SH2 domains have not been identified. It would seem, therefore, that SH2 signaling pathways arose very early in the evolution of multicellular organisms, perhaps to facilitate intercellular comunication.

Animals↗

PubMed1997

Gln 63 of Rho is deamidated by Escherichia coli cytotoxic necrotizing factor-1.

The actin cytoskeleton is regulated by GTP-hydrolysing proteins, the Rho GTPases, which act as molecular switches in diverse signal-transduction processes. Various bacterial toxins can inactivate Rho GTPases by ADP-ribosylation or glucosylation. Previous research has identified Rho proteins as putative targets for Escherichia coli cytotoxic necrotizing factors 1 and 2 (CNF1 and 2). These toxins induce actin assembly and multinucleation in culture cells. Here we show that treatment of RhoA with CNF1 inhibits the intrinsic GTPase activity of RhoA and completely blocks GTPase activity stimulated by the Rho-GTPase-activating protein (rhoGAP). Analysis by mass spectrometry and amino-acid sequencing of proteolytic peptides derived from CNF1-treated RhoA indicate that CNF1 induces deamidation of a glutamine residue at position 63 (Gln 63) to give constitutively active Rho protein.

3T3 Cells↗

PubMed1997

mRNA silencing in erythroid differentiation: hnRNP K and hnRNP E1 regulate 15-lipoxygenase translation from the 3' end.

Although LOX mRNA accumulates early during differentiation, a differentiation control element in its 3' untranslated region confers translational silencing until late stage erythropoiesis. We have purified two proteins from rabbit reticulocytes that specifically mediate LOX silencing and identified them as hnRNPs K and E1. Transfection of hnRNP K and hnRNP E1 into HeLa cells specifically silenced the translation of reporter mRNAs bearing a differentiation control element in their 3' untranslated region. Silenced LOX mRNA in rabbit reticulocytes specifically coimmunoprecipitated with hnRNP K. In a reconstituted cell-free translation system, addition of recombinant hnRNP K and hnRNP E1 recapitulates this regulation via a specific inhibition of 80S ribosome assembly on LOX mRNA. Both proteins can control cap-dependent and internal ribosome entry site-mediated translation by binding to differentiation control elements. Our data suggest a specific cytoplasmic function for hnRNPs as translational regulatory proteins.

Amino Acid Sequence↗

PubMed1997

FLICE is activated by association with the CD95 death-inducing signaling complex (DISC).

Upon activation, the apoptosis-inducing cell membrane receptor CD95 (APO-1/Fas) recruits a set of intracellular signaling proteins (CAP1-4) into a death-inducing signaling complex (DISC). In the DISC, CAP1 and CAP2 represent FADD/MORT1. CAP4 was identified recently as an ICE-like protease, FLICE, with two death effector domains (DED). Here we show that FLICE binds to FADD through its N-terminal DED. This is an obligatory step in CD95 signaling detected in the DISC of all CD95-sensitive cells tested. Upon prolonged triggering of CD95 with agonistic antibodies all cytosolic FLICE gets proteolytically activated. Physiological FLICE cleavage requires association with the DISC and occurs by a two-step mechanism. Initial cleavage generates a p43 and a p12 fragment further processed to a p10 fragment. Subsequent cleavage of the receptor-bound p43 results in formation of the prodomain p26 and the release of the active site-containing fragment p18. Activation of FLICE is blocked by the peptide inhibitors zVAD-fmk, zDEVD-fmk and zIETD-fmk, but not by crmA or Ac-YVAD-CHO. Taken together, our data indicate that FLICE is the first in a cascade of ICE-like proteases activated by CD95 and that this activation requires a functional CD95 DISC.

Adaptor Proteins, Signal Transducing↗

PubMed1997

Automation of matrix-assisted laser desorption/ionization mass spectrometry using fuzzy logic feedback control.

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is a sensitive and versatile method for biomolecular analysis which has potential for high-throughput screening in many applications. To obtain mass spectra of optimal quality, however, laser fluence is continuously adjusted during data acquisition to be close to the threshold level of ion production, requiring a skilled operator and several minutes of acquisition time per sample. Using real-time fuzzy logic control of the laser fluence, we here demonstrate that the acquisition of MALDI spectra can be automated without reduction of data quality. The control algorithm evaluates signal intensity and mass resolution of the base peak. It then regulates the laser fluence to keep the ion signal intensity within the dynamic range of the data acquisition hardware while maintaining high mass resolution. This fuzzy logic control system allows unattended data acquisition using either static ion extraction or delayed ion extraction MALDI. Even for difficult samples such as femtomole-level peptide mixtures, no significant reduction in data quality is observed, as compared to manually obtained spectra. Automated analysis of 78 chromatographic fractions with high mass accuracy demonstrates the utility of the method. The control algorithm has been combined with other software modules to completely automate database identification of proteins by their peptide mass maps. The success of fuzzy logic in MALDI automation suggests wider uses of this technique in mass spectrometry.

Automation↗

PubMed1997

Reverse transcriptase motifs in the catalytic subunit of telomerase.

Telomerase is a ribonucleoprotein enzyme essential for the replication of chromosome termini in most eukaryotes. Telomerase RNA components have been identified from many organisms, but no protein component has been demonstrated to catalyze telomeric DNA extension. Telomerase was purified from Euplotes aediculatus, a ciliated protozoan, and one of its proteins was partially sequenced by nanoelectrospray tandem mass spectrometry. Cloning and sequence analysis of the corresponding gene revealed that this 123-kilodalton protein (p123) contains reverse transcriptase motifs. A yeast (Saccharomyces cerevisiae) homolog was found and subsequently identified as EST2 (ever shorter telomeres), deletion of which had independently been shown to produce telomere defects. Introduction of single amino acid substitutions within the reverse transcriptase motifs of Est2 protein led to telomere shortening and senescence in yeast, indicating that these motifs are important for catalysis of telomere elongation in vivo. In vitro telomeric DNA extension occurred with extracts from wild-type yeast but not from est2 mutants or mutants deficient in telomerase RNA. Thus, the reverse transcriptase protein fold, previously known to be involved in retroviral replication and retrotransposition, is essential for normal chromosome telomere replication in diverse eukaryotes.

Amino Acid Sequence↗

PubMed1997

Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry.

Here we report the rapid identification of the proteins of the spliceosomal U1 small nuclear ribonucleoprotein (snRNP) from the yeast Saccharomyces cerevisiae by searching mass spectrometric data in genomic sequence databases. The U1 snRNP, containing a histidine-tagged 70K protein, was isolated from cell extracts by anti m3G-cap immunoaffinity and subsequent nickel nitrilotriacetic acid chromatography. A U1 snRNP fraction containing 20 proteins was obtained. Further purification by glycerol gradient centrifugation identified nine U1 snRNP specific and six common proteins. The U1 snRNP proteins were partially sequenced by nanoelectrospray mass spectrometry, and their genes were identified in the data base via multiple peptide sequence tags. Apart from the already known common proteins D1, D3, F, and G, the D2 and E homologs were also identified. The same six common proteins were detected in core U2 snRNP, which was purified and analyzed separately. The biochemical association of these six proteins with yeast snRNPs is shown here for the first time. Intriguingly, the Sm B/B' homolog was not detected. In addition to the well characterized yeast U1 specific proteins [U1-70K (Snp1p), U1-A (Mud1p), Prp39p, and Prp40p] the homolog of the U1-C protein was identified together with four additional novel U1 specific proteins, which are not found in mammalian U1. This is the first time that the components of a multiprotein complex from an organism with a sequenced genome have been characterized by mass spectrometry. The technique should be applicable to any protein complex that can be biochemically purified from an organism whose genome is known.

Amino Acid Sequence↗

PubMed1997

The Dose Reduction in Schizophrenia (DORIS) Study: a final report.

Twenty-one medication-free chronic schizophrenics were randomly assigned to three treatment groups: 50% blockade of the bromocriptine growth hormone (GH) response, 100% blockade or 10 ng/ml haloperidol. Only seven of the 21 patients showed a significant improvement after 6 weeks in positive psychotic symptoms; six of the seven responders came from the 50 and 100% blockade groups, suggesting greater efficacy at lower doses. Fifty percent blockade was associated with an average daily haloperidol dose of 3.2 mg and plasma haloperidol levels below the limit of detection (< 1 ng/ml). 100% blockade was associated with a daily dose of 6.5 mg and a plasma haloperidol level of 1 ng/ml. Negative symptoms significantly improved in only four of the 21 patients, and three of these patients were from the 100% blockade group. Twenty-nine patients currently receiving 20 mg/day haloperidol were randomly assigned to three treatment groups: placebo, 100% blockade of the GH response and 10 ng/ml. Patients in the placebo group showed significant deterioration along both the positive and negative symptom dimensions. There were no significant symptom differences between the 100% blockade and the 10 ng/ml groups. The patients in the 100% blockade group had on average a daily dose reduction from 20 to 11 mg/day and a 65% reduction in the plasma haloperidol level. There was a 70% difference in the average daily dose for 100% blockade between the two study arms. The higher daily dose in the dose-reduction arm may reflect receptor up-regulation and/or other "tolerance'-like mechanisms associated with chronic neuroleptic administration.

Adult↗

PubMed1997

Rapid 'de novo' peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer.

Protein microanalysis usually involves the sequencing of gel-separated proteins available in very small amounts. While mass spectrometry has become the method of choice for identifying proteins in databases, in almost all laboratories 'de novo' protein sequencing is still performed by Edman degradation. Here we show that a combination of the nanoelectrospray ion source, isotopic end labeling of peptides and a quadrupole/ time-of-flight instrument allows facile read-out of the sequences of tryptic peptides. Isotopic labeling was performed by enzymatic digestion of proteins in 1:1 16O/18O water, eliminating the need for peptide derivatization. A quadrupole/time-of-flight mass spectrometer was constructed from a triple quadrupole and an electrospray time-of-flight instrument. Tandem mass spectra of peptides were obtained with better than 50 ppm mass accuracy and resolution routinely in excess of 5000. Unique and error tolerant identification of yeast proteins as well as the sequencing of a novel protein illustrate the potential of the approach. The high data quality in tandem mass spectra and the additional information provided by the isotopic end labeling of peptides enabled automated interpretation of the spectra via simple software algorithms. The technique demonstrated here removes one of the last obstacles to routine and high throughput protein sequencing by mass spectrometry.

Databases, Factual↗

PubMed1997

Identification of components of trans-Golgi network-derived transport vesicles and detergent-insoluble complexes by nanoelectrospray tandem mass spectrometry.

Epithelial cells have to deliver newly synthesized proteins to the apical and the basolateral plasma membrane domains of the polarized cell surface. Sorting takes place in the trans-Golgi network and at least two vesicular carriers exist for apical and basolateral delivery. After immuno-isolation, the composition of these vesicle preparations was analyzed by two-dimensional (2-D) gel electrophoresis and detergent extraction. In this paper we compare the constituents of detergent-insoluble complexes in different cell lines of polarized or nonpolarized origin and present the identification of five previously uncharacterized proteins. We show that our protein identification strategy can be successfully applied to the problem of small hydrophobic proteins from organisms that have not been substantially sequenced. The high sensitivity of nanoelectrospray tandem mass spectrometry allowed us to identify two proteins that belong to the p23/p24 family of putative cargo receptors for vesicular trafficking. Furthermore we have mapped CD9 and CD81, two members of a large family of proteins consisting of highly hydrophobic four transmembrane proteins. In addition we have identified caveolin-2 as a constituent of basolateral transport vesicles. We have also extended our analysis of immuno-isolated vesicles to a more basic pI range and show that this region on 2-D gels is devoid of proteins. With these approaches and with the previously published data we have now identified most of the major low molecular weight proteins recovered in detergent-insoluble glycolipid-enriched complexes.

Amino Acid Sequence↗

PubMed1997

Improvement in specificity of [14C]d-xylose breath test for bacterial overgrowth.

The aim of the study was to determine whether the specificity of the [14C]d-xylose breath test could be improved, by excluding false-positive tests due to premature colonic metabolism of the [14C]d-xylose caused by rapid colonic transit. Forty-seven patients with suspected small bowel bacterial overgrowth were investigated by (1) aspiration and culture of duodenal fluid and (2) a [14C]d-xylose breath test. Those with either a positive duodenal culture or breath test had a repeat [14C]d-xylose breath test given with one of three transit markers (barium, Gastrografin or 99mTc-labeled tin colloid) to determine if the site of metabolism was in the small bowel or colon. Fourteen patients had positive duodenal cultures, four of whom had a negative [14C]d-xylose breath test, 15 patients had a positive [14C]d-xylose breath test, three of which were due to colonic metabolism of the xylose. Where transit markers were used, 14C was detectable in the breath and serum before barium had entered the small bowel, thus the barium did not comigrate with the xylose. Gastrografin accelerated small bowel transit, leading to malabsorption of the xylose in the small intestine and subsequent colonic metabolism of the xylose. 99mTc-labeled tin colloid had no obvious disadvantages and appeared to be the marker of choice. The use of a transit marker increased the specificity of the [14C]d-xylose breath test from 85% to 94%. The specificity of the [14C]d-xylose breath test for the detection of small bowel bacterial overgrowth is improved to greater than 90% by the use of an appropriate transit marker.

Bacteria↗

PubMed1997

Peptide sequencing by mass spectrometry for homology searches and cloning of genes.

It is now possible to obtain sequence information from gel-separated proteins by mass spectrometry at levels too low for conventional approaches. Usually this tandem mass spectrometric data are used for database searches with the aim of identifying the corresponding gene. Recently it has been shown that long and accurate amino acid sequences can be obtained which are sufficient for PCR-based strategies to clone the corresponding gene [Wilm et al. (1996), Nature 379, 466-469]. More than eight proteins have now been cloned based on that method. In many more cases the sequence information identified homologous proteins. Issues involved in cloning by mass spectrometric sequence information are discussed, as are two case studies. These results clearly establish mass spectrometry as a viable tool not only for the database identification of proteins, but also for the de novo sequencing of gel-separated proteins at the low-picomole to femtomole level.

Amino Acid Sequence↗

PubMed1997

Automated protein preparation techniques using a digest robot.

Since the introduction of fast analysis methods for peptide mixtures such as MALDI-MS, peptide micropreparation and digest methods have become an important bottleneck in the protein characterization process. We therefore developed and describe here a digest robot capable of processing 30 protein samples in parallel [Houthaeve et al. (1995), FEBS Lett. 376, 91-94]. Briefly, after gel pieces or blots are cut out, they are loaded in flowthrough reactors and these are loaded in a thermocontrolled reactor block. The proteins are then washed, reduced, and alkylated, proteolytically or chemically cleaved, and resulting peptides extracted. The system allows the parallel use of different reagents and enzymes during the same run, and is compatible with RP-HPLC peptide separation and Edman degradation, MALDI-MS, and NanoES-MS/MS. The digest robot is now also commercially available from ABIMED. In an ongoing project aimed at elucidating proteinaceous structures involved in the functional and structural maintenance of the Golgi apparatus, we illustrate the strength of the digest robot for the fast analysis of several proteins. We conclude that the performance of the digest robot is comparable to currently used manual digestion methods. The approach outlined makes sample preparation procedures faster, simpler, and less labor-intensive.

Chemistry Techniques, Analytical↗