A developmentally regulated gene product from Dictyostelium discoideum shows high homology to human alpha-L-fucosidase

Novel bifidobacterial glycosidases acting on sugar chains of mucin glycoproteins

Bifidobacterium bifidum was found to produce a specific 1,2-alpha-L-fucosidase. Its gene (afc A) has been cloned and the DNA sequence was determined. The Afc A protein consisting of 1959 amino acid residues with a predicted molecular mass of 205 kDa can be divided into three domains; the N-terminal function-unknown domain (576 aa), the catalytic domain (898 aa), and the C-terminal bacterial Ig-like domain (485 aa). The recombinant catalytic domain specifically hydrolyzed the terminal alpha-(1-->2)-fucosidic linkages of various oligosaccharides and sugar chains of glycoproteins. The primary structure of the catalytic domain exhibited no similarity to those of any glycoside hydrolases but showed similarity to those of several hypothetical proteins in a database, which resulted in establishment of a novel glycoside hydrolase family (GH family 95). Several bifidobacteria were found to produce a specific endo-alpha-N-acetylgalactosaminidase, which is the endoglycosidase liberating the O-glycosidically linked galactosyl beta1-->3 N-acetylgalactosamine disaccharide from mucin glycoprotein. The molecular cloning of endo-alpha-N-acetylgalactosaminidase was carried out on Bifidobacterium longum based on the information in the database. The gene was found to comprise 1966 amino acid residues with a predicted molecular mass of 210 kDa. The recombinant protein released galactosyl beta1-->3 N-acetylgalactosamine disaccharide from natural glycoproteins. This enzyme of B. longum is believed to be involved in the catabolism of oligosaccharide of intestinal mucin glycoproteins. Both 1,2-alpha-L-fucosidase and endo-alpha-N-acetylgalactosaminidase are novel and specific enzymes acting on oligosaccharides that exist mainly in mucin glycoproteins. Thus, it is reasonable to conclude that bifidobacteria produce these enzymes to preferentially utilize the oligosaccharides present in the intestinal ecosystem.

Molecular cloning and characterization of Bifidobacterium bifidum 1,2-alpha-L-fucosidase (AfcA), a novel inverting glycosidase (glycoside hydrolase family 95)

A genomic library of Bifidobacterium bifidum constructed in Escherichia coli was screened for the ability to hydrolyze the alpha-(1-->2) linkage of 2'-fucosyllactose, and a gene encoding 1,2-alpha-l-fucosidase (AfcA) was isolated. The afcA gene was found to comprise 1,959 amino acid residues with a predicted molecular mass of 205 kDa and containing a signal peptide and a membrane anchor at the N and C termini, respectively. A domain responsible for fucosidase activity (the Fuc domain; amino acid residues 577 to 1474) was localized by deletion analysis and then purified as a hexahistidine-tagged protein. The recombinant Fuc domain specifically hydrolyzed the terminal alpha-(1-->2)-fucosidic linkages of various oligosaccharides and a sugar chain of a glycoprotein. The stereochemical course of the hydrolysis of 2'-fucosyllactose was determined to be inversion by using (1)H nuclear magnetic resonance. The primary structure of the Fuc domain exhibited no similarity to those of any glycoside hydrolases (GHs) but showed high similarity to those of several hypothetical proteins in a database. Thus, it was revealed that the AfcA protein constitutes a novel inverting GH family (GH family 95).

Identification and analysis of catalytic TIM barrel domains in seven further glycoside hydrolase families

Fold recognition results allocate catalytic triose phosphate isomerase (TIM) barrels to seven previously unassigned glycoside hydrolase (GH) families, numbers 29, 44, 50, 71, 84, 85 and 89, enabling prediction of catalytic residues. Modelling of GH family 50 suggests that it may be the common evolutionary ancestor of families 42 and 14. TIM barrels now comprise the catalytic domains of more than half of the assigned GH families, and catalyse a much larger variety of GH reactions than any other catalytic domain architecture. Only 327 GH sequences still have no structurally identified catalytic domain.

Sperm-egg binding mediated by sperm alpha-L-fucosidase in the ascidian, Halocynthia roretzi

Spermatozoa bind to the vitelline coat in the ascidians and many other animals. The binding of sperm in Halocynthia roretzi is mediated by a sperm alpha-L-fucosidase and complementary-L-fucosyl residues of glycoproteins in the vitelline coat. cDNA clones for alpha-L-fucosidase were isolated from growing testis mRNA. It contained a 1398 bp full-length cDNA insert (HrFuc'ase) that encoded the 466 amino acid residues of H. roretzi sperm alpha-L-fucosidase. A putative signal peptide of 21 amino acid residues proceeded the sequence for the mature protein (M.W. 52.4 kDa). The coding sequence for HrFuc'ase showed 47.7% sequence identity to the human liver fucosidase sequence. The polyclonal antibody was prepared against a lacZ-HrFuc'ase fusion protein expressed in E. coli. The antibody crossed to a 54 kDa protein in sperm on western blotting and inhibited fertilization in a dose dependent manner. These data suggest that sperm-egg binding is mediated by the sperm alpha-L-fucosidase, HrFuc'ase in the ascidian, H. roretzi.

Combined use of ESI-MS and UV diode-array detection for localization of disulfide bonds in proteins: application to an alpha-L-fucosidase of pea

A simplified strategy is described for the assignment of disulfide bonds in proteins of medium to high molecular mass (10-30 kDa). The method combines the use of high-performance liquid chromatography coupled to electrospray ionization mass spectrometry (HPLC-ESI-MS) and HPLC with UV diode-array detection (HPLC diode array). The denatured protein is subjected to proteolysis and the peptide mixture is divided into three fractions: (i) underivatized peptides, (ii) ethylpyridylated peptides, and (iii) reduced and ethylpyridylated peptides. The three peptide ensembles are then subjected to chromatographic and spectroscopic analysis. A systematic methodology is described to analyze the large amount of data obtained. The method was applied to the localization of disulfide bonds in alpha-L-fucosidase from pea. The two disulfide bonds were located between residues Cys64 and Cys109 and between Cys162 and Cys169, while Cys127 was free.

Nonradioactive immunoquantification of alpha-L-fucosidase protein in human colon tissues

alpha-L-Fucosidase is a glycosidase involved in the degradation of fucoglycoconjugates and has a diagnostic significance because it has been described to be altered in several known diseases. However, in vitro studies on enzymatic activities may not reflect the real protein levels in tissues. This paper describes a simple method to quantify alpha-L-fucosidase protein levels in human crude extracts, combining the slot-blot technique and a nonradioactive immunoassay. Taking advantage of the similarities in different mammalian fucosidases, a polyclonal antiserum was raised against commercial purified alpha-L-fucosidase from bovine kidney that cross-reacted with the human colon enzyme. The method is able to detect as little as 0.75 ng alpha-L-fucosidase. To illustrate the direct application of this technique, we analysed and quantified alpha-L-fucosidase protein levels in 18 human colon crude samples. This technique could prove useful in clinical pathology, allowing fast and accurate measurement of alpha-L-fucosidase in crude extracts.

A cis-acting element responsible for early gene induction by extracellular cAMP in Dictyostelium discoideum

We have analysed the promoter of the Dictyostelium discoideum alpha-L-fucosidase (ALF) gene, and have identified a 58 bp fragment responsible for transcriptional activation mediated by extracellular cAMP. Replacement of regulatory sequences in the cAMP-independent actin 15 promoter by this fragment confers cAMP regulation to the hybrid promoter. A cAMP analog with high affinity to the cell surface cAMP receptor can induce transcription from the endogenous as well as from the hybrid promoter. Gel-shift experiments show that the 58 bp fragment is a target for nuclear DNA-binding proteins, and that a specific complex is formed in response to cAMP stimulation. The major cAMP-dependent DNA.protein complex is formed with a 22 bp subfragment which we have termed DCRE (Dictyostelium cAMP responsive element).

Mammalian alpha-L-fucosidases

Mammalian alpha-L-fucosidases are a ubiquitous group of relatively large multimeric lysosomal glycosidases involved in the degradation of a diverse group of naturally-occurring fucoglycoconjugates. These enzymes are closely related structurally as indicated by immunochemical cross-reactivity and cloning studies. Mammalian fucosidases are sialoglycoproteins and the carbohydrate, particularly sialic acid, contributes to producing multiple isoforms which can differ in various species as well as in different tissues within a given species. alpha-L-Fucosidases exhibit maximal activity at pH values between 4 and 7, have similar kinetic properties with synthetic substrates (PNP-fucoside and 4-MU-fucoside), and exhibit broad substrate specificity on natural substrates. Numerous linkages (alpha 1-2, alpha 1-3, alpha 1-4, alpha 1-6), primarily to galactose and N-acetylglucosamine, can be hydrolyzed but preference is often seen for small mol. wt water-soluble substrates with fucose in alpha 1-2 linkage to galactose. The importance of alpha-L-fucosidase in mammalian metabolism is evidenced by deficiency or absence of its enzymatic activity leading to a fatal genetic disease, at least in humans and English Springer Spaniels.

The molecular basis for alternative splicing of the CABP1 transcripts in Dictyostelium discoideum

We have determined the nucleotide sequence of the CABP1 gene from Dictyostelium discoideum. Together with previous data on cDNA sequences, we establish that alternative splicing of transcripts derived from this gene is responsible for the production of the two CABP1 subunits. RNA blot analysis suggested that alternative splicing of the CABP1 transcripts occurs during growth and throughout development. In addition, we have compiled the intron sequences of Dictyostelium pre-mRNAs and observed that the GUAAGU hexanucleotide at the 5' splice site is highly conserved. The 5' splice site of CABP1 deviates from the consensus hexanucleotide in having a sequence of GUAAUA. To assess the role of the modified 5' splice on differential splicing, we have constructed an actin-CABP1 fusion gene and transformed it into Dictyostelium cells. Analysis by immunoprecipitation, with anti-CABP1 antibody and amplification of specific cDNAs by polymerase chain reaction show that the transcripts generated by the fusion gene are alternatively spliced. When the 5' splice site of the fusion gene is mutated to conform to the consensus sequence, the resulting transcripts are constitutively spliced. These observations suggest that changes in positions 5 and 6 of the donor splice site are involved in the alternative splicing of the CABP1 transcripts.

Nuclear pre-mRNA introns: analysis and comparison of intron sequences from Tetrahymena thermophila and other eukaryotes

We have sequenced 14 introns from the ciliate Tetrahymena thermophila and include these in an analysis of the 27 intron sequences available from seven T. thermophila protein-encoding genes. Consensus 5' and 3' splice junctions were determined and found to resemble the junctions of other nuclear pre-mRNA introns. Unique features are noted and discussed. Overall the introns have a mean A + T content of 85% (21% higher than neighbouring exons) with smaller introns tending towards a higher A + T content. Approximately half of the introns are less than 100 bp. Introns from other organisms (approximately 30 of each) were also examined. The introns of Dictyostelium discoideum, Caenorhabditis elegans and Drosophila melanogaster, like those of T. thermophila, have a much higher mean A + T content than their neighbouring exons (greater than 20%). Introns from plants, Neurospora crassa and Schizosaccharomyces pombe also have a significantly higher A + T content (10%-20%). Since a high A + T content is required for intron splicing in plants (58), the elevated A + T content in the introns of these other organisms may also be functionally significant. The introns of yeast (Saccharomyces cerevisiae) and mammals (humans) appear to lack this trait and thus in some aspects may be atypical. The polypyrimidine tract, so distinctive of vertebrate introns, is not a trait of the introns in the non-vertebrate organisms examined in this study.

Regulation of the Discoidin I gamma gene in Dictyostelium discoideum: identification of individual promoter elements mediating induction of transcription and repression by cyclic AMP

We dissected the promoter of the developmentally induced and cyclic AMP-repressed discoidin I gamma gene and identified a sequence element essential for developmental induction. Transfer of the element to an inactive heterologous promoter demonstrated that this sequence is sufficient to confer expression in axenically growing cells and to induce gene activity in development after growth on bacteria. A 16-base-pair sequence within this element was shown to be sufficient for induction in the discoidin promoter context and was used to reactivate different truncated promoter constructs. This led to the localization of an element necessary for down regulation of gene expression by extracellular cyclic AMP.

Regulation of the Discoidin I gamma gene in Dictyostelium discoideum: identification of individual promoter elements mediating induction of transcription and repression by cyclic AMP

We dissected the promoter of the developmentally induced and cyclic AMP-repressed discoidin I gamma gene and identified a sequence element essential for developmental induction. Transfer of the element to an inactive heterologous promoter demonstrated that this sequence is sufficient to confer expression in axenically growing cells and to induce gene activity in development after growth on bacteria. A 16-base-pair sequence within this element was shown to be sufficient for induction in the discoidin promoter context and was used to reactivate different truncated promoter constructs. This led to the localization of an element necessary for down regulation of gene expression by extracellular cyclic AMP.

Identification of a cis-acting element controlling induction of early gene expression in Dictyostelium discoideum

Using a new promoter analysis transformation vector for Dictyostelium discoideum (PAV-CAT), we have defined cis-acting elements in the promoter of the cyclic AMP-induced early-expressed gene A11H2, which encodes an alpha-fucosidase-related protein (A. Müller-Taubenberger, M. Westphal, A. Noegel, and G. Gerisch, FEBS Lett. 246:185-192, 1989). Sequences responsible for developmentally regulated gene induction could be separated from the basal promoter that conferred low levels of transcriptional activity. By gel shift experiments, we present evidence that the cis-acting element is the target of a trans-acting factor that by itself is subject to developmental regulation.

Isolation and sequence analysis of a cDNA encoding rat liver alpha-L-fucosidase

cDNA clones for alpha-L-fucosidase were isolated from a rat liver lambda gt11 expression library by using both monospecific polyclonal antibodies against the affinity-purified enzyme and biotinylated rat liver fucosidase cDNA sequences as probes. The largest clone, lambda FC9, contained a 1522 bp full-length cDNA insert (FC9) that encoded the 434-amino acid-residue subunit (Mr 50439) of rat liver alpha-L-fucosidase. A putative signal peptide 28 amino acid residues in length preceded the sequence for the mature protein. In addition, FC9 specified for 11 nucleotide residues of 5' untranslated sequence, 78 nucleotide residues of 3' untranslated sequence and a poly(A) tail. The deduced amino acid sequence from FC9 in conjunction with the experimentally determined N-terminus of the mature enzyme suggested that rat liver fucosidase did not contain a pro-segment. However, there was the possibility of limited N-terminal processing (one to five amino acid residues) having occurred after removal of the predicted signal peptide. Amino acid sequences deduced from FC9 were co-linear with amino acid sequences measured at the N-terminus of purified fucosidase and on two of its CNBr-cleavage peptides. An unusual aspect of rat liver alpha-L-fucosidase protein structure obtained from the FC9 data was its high content of tryptophan (6%). The coding sequence from FC9 showed 82% sequence identity with that from a previously reported incomplete human fucosidase sequence [O'Brien, Willems, Fukushima, de Wet, Darby, DiCioccio, Fowler & Shows, (1987) Enzyme 38, 45-53].

Identification of a cis-acting element controlling induction of early gene expression in Dictyostelium discoideum

Using a new promoter analysis transformation vector for Dictyostelium discoideum (PAV-CAT), we have defined cis-acting elements in the promoter of the cyclic AMP-induced early-expressed gene A11H2, which encodes an alpha-fucosidase-related protein (A. Müller-Taubenberger, M. Westphal, A. Noegel, and G. Gerisch, FEBS Lett. 246:185-192, 1989). Sequences responsible for developmentally regulated gene induction could be separated from the basal promoter that conferred low levels of transcriptional activity. By gel shift experiments, we present evidence that the cis-acting element is the target of a trans-acting factor that by itself is subject to developmental regulation.