Biomedical subjects

J Robben

Publications and source records attributed to J Robben.

At least 19 recordsLinked to original sources

PubMed2005

Functional display of family 11 endoxylanases on the surface of phage M13.

Two family 11 endoxylanases (EC 3.2.1.8) were functionally displayed on the surface of bacteriophage M13. The genes encoding endo-1,4-xylanase I from Aspergillus niger (ExlA) and endo-1,4-xylanase A from Bacillus subtilis (XynA) were fused to the gene encoding the minor coat protein g3p in phagemid vector pHOS31. Phage rescue resulted in functional monovalent display of the enzymes as was demonstrated by three independent tests. Firstly, purified recombinant phage particles showed a clear hydrolytic activity in an activity assay based on insoluble, chromagenic arabinoxylan substrate. Secondly, specific binding of endoxylanase displaying phages to immobilized endoxylanase inhibitors was demonstrated by interaction ELISA. Finally, two rounds of selection and amplification in a biopanning procedure against immobilized endoxylanase inhibitor were performed. Phages displaying endoxylanases were strongly enriched from background phages displaying unrelated proteins. These results open perspectives to use phage display for analysing protein-protein interactions at the interface between endoxylanases and their inhibitors. In addition, this technology should enable engineering of endoxylanases into novel variants with altered binding properties towards endoxylanase inhibitors.

Aspergillus niger↗

PubMed2005

Protein profiling of 3T3-L1 adipocyte differentiation and (tumor necrosis factor alpha-mediated) starvation.

The increased incidence of obesity and related disorders in Western societies requires a thorough understanding of the adipogenic process. Data at the protein level of this process are scarce. Therefore we performed a proteome analysis of differentiating and starving 3T3-L1 cells using two-dimensional gel electrophoresis combined with mass spectrometry. Effects of different starvation conditions were examined by subjecting 3T3-L1 adipocytes to caloric restriction, either in the absence or the presence of the lipolysis inducer tumor necrosis factor-alpha. Ninety-three differentially expressed proteins were found during differentiation and starvation of 3T3-L1 cells, 50 of which were identified. GenMAPP/MAPP-finder software revealed a non-reciprocal regulation of the glycolytic pathway during 3T3-L1 differentiation followed by starvation. Furthermore, proteins involved in growth regulation, cytoskeletal rearrangements and protein modification, 16 of which have not been described before in 3T3-L1 cells, were identified. In conclusion, our data provide valuable information for further understanding of the adipogenic process.

3T3-L1 Cells↗

PubMed2004

Approach for defining endogenous reference genes in gene expression experiments.

The quantification of gene expression by real-time polymerase chain reaction (PCR) has revolutionized the field of gene expression analysis. Due to its sensitivity and flexibility it is becoming the method of choice for many investigators. However, good normalization protocols still have to be implemented to facilitate data exchange and comparison. We have designed primers for 10 unrelated genes and developed a simple protocol to detect genes with stable expression that are suitable for use as endogenous reference genes for further use in the normalization of gene expression data obtained by real-time PCR. Using this protocol, we were able to identify human proteosome subunit Y as a reliable endogenous reference gene for human umbilical vein endothelial cells treated for up to 18 h with TNFalpha, IL-4, or IFNgamma and for B cells isolated from healthy controls and patients suffering from IgA nephropathy. Other optional endogenous reference genes that can be considered are phosphomannomutase (PPMM) and actin for endothelial cells and glyceraldehyde-3-phosphate dehydrogenase and PPMM for B cells.

Endothelial Cells↗

PubMed2004

Profiling of the secreted proteins during 3T3-L1 adipocyte differentiation leads to the identification of novel adipokines.

Adipose tissue is an endocrine organ capable of secreting a number of adipokines with a role in the regulation of adipose tissue and whole-body metabolism. We used two-dimensional gel electrophoresis combined with mass spectrometry to profile the secreted proteins from (pre)adipocytes. The culture medium of 3T3-L1 cells during adipocyte differentiation was screened, and 41 proteins that responded to blocking of secretion by 20 degrees C treatment and/or brefeldin A treatment were identified. Prohibitin, stress-70 protein, and adhesion-regulating molecule 1 are reported for the first time as secreted proteins. In addition, procollagen C-proteinase enhancer protein, galectin-1, cyclophilin A and C, and SF20/IL-25 are newly identified as adipocyte secreted factors. Secretion profiles indicated a dynamic environment including an actively remodeling extracellular matrix and several factors involved in growth regulation.

3T3-L1 Cells↗

PubMed2004

Identification and characterization of a highly thermostable bacteriophage lysozyme.

Pseudomonas aeruginosa bacteriophage phiKMV is a T7-like lytic phage. Liquid chromatography-mass spectrometry of the structural proteins revealed gene product 36 (gp36) as part of the phiKMV phage particle. The presence of a lysozyme domain in the C terminal of this protein (gp36C) was verified by turbidimetric assays on chloroform-treated P. aeruginosa PAO1 and Escherichia coli WK6 cells. The molecular mass (20,884 Da) and pI (6.4) of recombinant gp36C were determined, as were the optimal enzymatic conditions (pH 6.0 in 16.7 mM phosphate buffer) and activity (4800 U/mg). Recombinant gp36C is a highly thermostable lysozyme, retaining 26% of its activity after 2 h at 100 degrees C and 21% after autoclaving. This thermostability could prove an interesting characteristic for food conservation technology.

Amino Acid Sequence↗

PubMed2002

The genome sequence of Schizosaccharomyces pombe.

We have sequenced and annotated the genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization.

Base Sequence↗

PubMed2001

Design and development of a new program for data processing of mass spectra acquired by means of a high-resolution double-focusing glow-discharge mass spectrometer.

An new program has been developed and implemented for data analysis of mass spectra obtained by use of the VG9000 glow-discharge mass spectrometer. The program, designed to run in a Windows 9X environment includes several tools for import and export of data, cluster generators, etc. An automated technique for the interpretation of mass spectra is also built into the program; this enables faster and operator-independent interpretation. When major interferences or not-well defined signals are involved, the automated technique might fail to find the correct result. Therefore, a manual, VG9000 software-like, bypass is at hand. A comparison of the different techniques and programs shows, in general, comparable results. An installable version of the software is available on the university FTP-server (ftp://PLASMA-FTP.uia.ac.be/ private/imsas/).

Journal Article↗

PubMed2000

Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.

The genome of the model plant Arabidopsis thaliana has been sequenced by an international collaboration, The Arabidopsis Genome Initiative. Here we report the complete sequence of chromosome 5. This chromosome is 26 megabases long; it is the second largest Arabidopsis chromosome and represents 21% of the sequenced regions of the genome. The sequence of chromosomes 2 and 4 have been reported previously and that of chromosomes 1 and 3, together with an analysis of the complete genome sequence, are reported in this issue. Analysis of the sequence of chromosome 5 yields further insights into centromere structure and the sequence determinants of heterochromatin condensation. The 5,874 genes encoded on chromosome 5 reveal several new functions in plants, and the patterns of gene organization provide insights into the mechanisms and extent of genome evolution in plants.

Animals↗

PubMed2000

Diagnostic accuracy of DNA image cytometry and urinary cytology with cells from voided urine in the detection of bladder cancer.

OBJECTIVES: To assess the potential of DNA image cytometry in screening for bladder cancer, compare it with conventional urinary cytology, and evaluate its possible use in routine urinary evaluation. Urinary cytology is still the most common method for detection of bladder cancer in routine clinical use. The considerable shortcomings of urinary cytology include its low sensitivity in low-grade carcinomas and its poor reproducibility. METHODS: Spontaneously voided urine specimens from 40 patients with grade 1 (n = 27), grade 2 (n = 10), and grade 3 (n = 3) histologically proven transitional cell carcinoma and 40 patients with symptomatic urologic disease of the bladder were analyzed by cytology and DNA image cytometry. The DNA content was determined by use of the CM-1 Cytometer according to the guidelines in the ESACP Consensus Report on Standardization of DNA Image Cytometry. RESULTS: Urinary cytology yielded an overall sensitivity of 47.5%. Conventional analysis of DNA histograms measuring the presence of DNA stemline aneuploidy (1.8c > stemline ploidy [STP] > 2.2c) revealed a sensitivity of 62.5%; applying the stemline interpretation according to Böcking et al. increased the overall sensitivity to 75%. The specificity of both methods was 100%. DNA image cytometry demonstrated a high sensitivity in grade 1 tumors (70.4%) compared with cytology (26%). CONCLUSIONS: In light of its highly improved sensitivity compared with urinary cytology, DNA image cytometry should be used to evaluate suspect urothelial cells in urinary cytology specimens. Since the method provides more objective and reproducible results with a specificity comparable to that of cytology, we encourage its primary application in the screening for bladder cancer, provided these results can be confirmed in a multicenter evaluation study.

Adult↗

PubMed2000

Progress in Arabidopsis genome sequencing and functional genomics.

Arabidopsis thaliana has a relatively small genome of approximately 130 Mb containing about 10% repetitive DNA. Genome sequencing studies reveal a gene-rich genome, predicted to contain approximately 25000 genes spaced on average every 4.5 kb. Between 10 to 20% of the predicted genes occur as clusters of related genes, indicating that local sequence duplication and subsequent divergence generates a significant proportion of gene families. In addition to gene families, repetitive sequences comprise individual and small clusters of two to three retroelements and other classes of smaller repeats. The clustering of highly repetitive elements is a striking feature of the A. thaliana genome emerging from sequence and other analyses.

Agriculture↗

PubMed1999

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.

The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.

Animals↗

PubMed1998

Misfolding of chloramphenicol acetyltransferase due to carboxy-terminal truncation can be corrected by second-site mutations.

Folding of chloramphenicol acetyltransferase (CAT) in Escherichia coli is hampered by deletion of the carboxy-terminal tail including the last residue of the carboxy-terminal alpha-helix. Such truncated CAT polypeptides quantitatively aggregate into cytoplasmic inclusion bodies, which results in absence of a chloramphenicol-resistant phenotype for the producing host. In this paper, a genetic approach is presented to examine this aggregation process in more detail. Random mutagenesis of inactive CAT followed by direct phenotypic selection for revertants with restored chloramphenicol resistance was used to isolate second-site suppressors of inactive truncation mutants of CAT. Two random mutagenesis procedures, independently of each other, yielded a unique substitution of Phe for Leu at amino acid position 145. This second-site mutation does not drastically affect the proteins' stability under normal growth conditions of E. coli. Hence, the introduction of Phe at amino acid position 145 improves the ability of the protein to fold into a soluble, enzymatically active conformation. The conservative character of the Leu145Phe replacement indicates that limited changes at crucial positions can have important effects on protein folding in vivo.

Chloramphenicol O-Acetyltransferase↗

PubMed1997

Sequence analysis of a near-subtelomeric 35.4 kb DNA segment on the right arm of chromosome VII from Saccharomyces cerevisiae carrying the MAL1 locus reveals 15 complete open reading frames, including ZUO1, BGL2 and BIO2 genes and an ABC transporter gene.

The nucleotide sequence of 35,400 bp at approximately 10 kb from the right telomere of chromosome VII was determined. The segment contains the MAL1 locus, one of the five unlinked loci sufficient for maltose utilization. Until now, each of these loci was considered to contain three genes (for regulator, permease and alpha-glucosidase), but a fourth gene, presumably an extra alpha-glucosidase gene, was found at MAL1 adjacent to the usual cluster of three genes. The two glucosidase genes are present in opposite orientation, forming an inverted repeat structure. In addition to the four genes at MAL1, there are 11 complete, non-overlapping open reading frames (ORFs) longer than 300 bp in the sequence presented here. A new ABC transporter gene (YGR281w), required for oligomycin resistance was found (YOR1; Katzman et al., 1995), and the previously sequenced BGL2 (YGR282c), ZUO1 (YGR285c) and BIO2 (YGR286c) genes were located. The sequence of BIO2, a biotin synthetase gene, required substantial correction and the size of Bio2p is 375, rather than 356, amino acids. Two ORFs show rather weak similarities to animal genes: YGR278w to an unknown ORF of Caenorhabditis elegans and YGR284c to the murine Surf-4, a member of a cluster of at least four housekeeping genes. The remaining five ORFs do not encode known functions, but three of these show weak to high similarities to other ORFs in the Saccharomyces cerevisiae genome and one (YGR280c) codes for a particularly lysine-rich protein.

ATP-Binding Cassette Transporters↗

PubMed1997

The sequence of a nearly unclonable 22.8 kb segment on the left arm chromosome VII from Saccharomyces cerevisiae reveals ARO2, RPL9A, TIP1, MRF1 genes and six new open reading frames.

The nucleotide sequence of 22,803 bp on the left arm of chromosome VII was determined by polymerase chain reaction-based approaches to compensate for the unstable character of cosmid clones from this region of the chromosome. The coding density of the sequence is particularly high (more than 83%). Twelve open reading frames (ORFs) longer than 300 bp were found, two of which (at the left side) have been described previously (James et al., 1995) after sequencing of an overlapping cosmid. Four other ORFs correspond to published sequences of the known genes ARO2, RPL9A, TIP1 and MRF1. ARO2 codes for chorismate synthetase. RPL9A for protein L9 of the large ribosomal subunit and MRF1 for a mitochondrial translation release factor. The TIP1 product interacts with Sec20p and is thus involved in transport from endoplasmic reticulum to Golgi. Five of the remaining ORFs have not been identified previously, while the sixth (YGL142c) has been partially sequenced as it lies 5' upstream of MRF1. These six ORFs are relatively large (between 933 and 3657 nucleotides). YGL146c, YGL142c, YGL140c and YGL139w have no significant homology to any protein sequence presently available in the public databases, but show two, nine, nine and eight putative transmembrane spans, respectively. YGL144c has a serine active site signature of lipases. YGL141w has limited homology to several human proteins, one of which mediates complex formation between papillomavirus E6 oncoprotein and tumor suppressor protein p53.

Arabidopsis Proteins↗

PubMed1996

Identification of local carboxy-terminal hydrophobic interactions essential for folding or stability of chloramphenicol acetyltransferase.

The role of the carboxy terminal in folding and stabilization of type I chloramphenicol acetyltransferase (CAT1) has been studied by mutagenesis and Fourier transform infrared analysis. We have shown that a CAT mutant truncated by seven amino acid residues folds into active protein. In this study, the last three residues of this truncated CAT mutant were randomized to detect structural information required for achieving a native enzyme conformation. Statistical analysis of sequencing data from randomly chosen mutants revealed that the amino-terminal CAT fragment of 212 amino acid residues is the shortest deletion mutant able to adopt a soluble, enzymatically active structure. This minimal length corresponds to a protein with full-length alpha5-helix in the three-dimensional crystal structure of CAT type III. The amino acid preferences at the carboxy terminal in the randomization experiments suggest that this helix also forms completely in the shortened CAT mutants. In addition correct folding and/or stabilization requires the formation of a hydrophobic + microdomain at the end of the alpha5-helix. The role of this hydrophobic interaction in CAT folding and structure stabilization is discussed.

Amino Acid Sequence↗

PubMed1995

Insertional re-activation of a chloramphenicol acetyltransferase misfolding mutant protein.

The deletion of nine residues from the C-terminus of the bacterial chloramphenicol acetyltransferase (CAT) results in deposition of the mutant protein in cytoplasmic inclusion bodies and loss of chloramphenicol resistance in Escherichia coli. This folding defect is relieved by C-terminal fusion of the polypeptide with as few as two residues. Based on these observations, efficient positive selection for the cloning of DNA fragments has been demonstrated. The cloning vector encodes a C-terminally truncated CAT protein. Restriction sites in front of the stop codon allow the insertion of target DNA, resulting in the production of properly folded CAT fusion proteins and regained chloramphenicol resistance. The positive selection of recombinants is accomplished by growth of transformants on chloramphenicol-containing agar plates. The method appears particularly convenient for the cloning of DNA fragments amplified by the PCR because minimal information to restore CAT folding can be included in the primers. The cloning of random sequences shows that the folding defect can be relieved by fusion to a wide variety of peptides, providing great flexibility to the positive selection system. This vector may also contribute to the determination of the role of the C-terminus in CAT folding.

Amino Acid Sequence↗

PubMed1993

Carboxyl terminus is essential for intracellular folding of chloramphenicol acetyltransferase.

Chloramphenicol acetyltransferase (CAT, EC 2.3.1.28) is a bacterial chloramphenicol resistance marker that is commonly used as a reporter enzyme in gene expression studies and as a carrier protein for the production of fused peptides. The latter can be done by insertion of target sequences into the native ScaI site near the 3'-end of the Tn9 cat gene. CAT activity in the resulting fusion proteins is retained. We observed that creation of a stop codon at this ScaI, which causes a COOH-terminal 9-amino acid deletion, results in loss of chloramphenicol resistance and total deposition of the mutant protein in inclusion bodies in Escherichia coli. Cytoplasmic solubility and enzyme activity are completely regained by elongation of this mutant with only 2 residues. Apparently, terminal residues of the alpha 5-helix play a crucial role in achieving the native conformation of nascent CAT molecules. Thus, CAT provides an interesting model system for mutational analysis of protein folding in vivo.

Amino Acid Sequence↗

PubMed1993

Two Streptomyces lividans 66 transfer RNA genes with anticodons corresponding to serine (AGC) and arginine (CGU) codons.

From the nucleotide sequence of a 2110-bp Streptomyces lividans 66 DNA fragment two transfer RNA genes were identified: tRNA(Ser) (AGC) and tRNA(Arg) (CGU). These tRNA genes are transcribed from the same DNA strand and both are preceded by a putative promoter structure. They are separated by an intergenic region of 191 bp. Like most Streptomyces tRNA genes described so far, they do not encode the 3' terminal CCA of mature tRNAs. Both genes are followed by extensive inverted repeats, which could serve as transcriptional terminator signals. Remarkably, these hairpin structures share an identical 9 base pair stretch (5'-GAAGCCCCG-3'). Furthermore, the tRNA(Arg) region is followed by two potential open reading frames, which are encoded on complementary strands and have 3' overlapping ends. The gene for tRNA(Arg) (CGU) is the first Streptomyces tRNA gene described so far which encodes the translation of a codon with uridine at the third (wobble) position.

Anticodon↗