Cloning of the gene encoding the catalytic subunit of casein kinase II from the yeast Yarrowia lipolytica

Casein kinase II from the yeast Yarrowia lipolytica is a heterotetramer of the form αα′β₂. We report on the cloning and sequencing of a partial cDNA and of the complete genomic DNA coding for the catalytic α subunit of the casein kinase II from this yeast species. The sequence of the gene coding for this enzyme has been analyzed. No intron was found in the gene, which is present in a single copy. The deduced amino acid sequence of the gene shows high similarity with those of α subunit described in other species, although, uniquely, Y. lipolytica CKIIα lacks cysteines. We find that the α subunit sequence of Y. lipolytica CKII is shown greater homology with the corresponding protein from S. pombe than with that from S. cerevisiae. We have analyzed CKIIα expression and CKIIα activity. We show that expression of this enzyme is regulated. The catalytic subunit is translated from a single mRNA, and the enzyme is present at a very low level in Y. lipolytica, as in other yeasts. Received: 20 December1997 / Accepted: 19 June 1997     

Tip-α (<Emphasis Type="Italic">hp0596</Emphasis> Gene Product) Is a Highly Immunogenic <Emphasis Type="Italic">Helicobacter pylori</Emphasis> Protein Involved in Colonization of Mouse Gastric Mucosa

A product of the Helicobacter pylori hp0596 gene (Tip-α) is a highly immunogenic homodimeric protein, unique for this bacterium. Cell fractionation experiments indicate that Tip-α is anchored to the inner membrane. In contrast, the three-dimensional model of the protein suggests that Tip-α is soluble or, at least, largely exposed to the solvent. hp0596 gene knockout resulted in a significant decrease in the level of H. pylori colonization as measured by real-time PCR assay. In addition, the Tip-α recombinant protein was determined to stimulate macrophage to produce IL-1α and TNF-α. Both results imply that Tip-α is rather loosely connected to the inner membrane and potentially released during infection.     

Evolution of the scrambled germline gene encoding α-telomere binding protein in three hypotrichous ciliates

The micronuclear genes encoding α-telomere-binding protein (αTP) in Oxytricha trifallax and Stylonychia mytilus contain multiple internal eliminated segments, or IESs, that divide the gene into multiple parts called macronuclear destined segments, or MDSs. The MDSs have become disordered, or scrambled, during evolution. The scrambled structures of the αTP genes in Oxytricha trifallax and S. mytilus have been compared with the previously published scrambled structure of the αTP gene in O. nova. The scrambled patterns of the αTP gene in the three species are similar but show significant differences. The micronuclear genes in O. nova and S. mytilus consist of 13 IESs and 14 MDSs, but the gene in O. trifallax is divided into three additional MDSs by the presence of three additional IESs, believed to have been inserted into the O. trifallaxαTP gene after divergence of O. trifallax from the other two species. Corresponding IESs among the three species have shifted along the DNA during evolution, presumably by a mutational mechanism that changes the short repeat sequences that flank IESs. The IESs also have changed markedly in length by insertion and/or deletion of nucleotides. Comparison of the putative αTP amino acid sequences in the three species reveals three conserved and three nonconserved domains. The 5′ nontranslated regions of the gene-sized molecules encoding αTP contain several conserved segments, and the 3′ nontranscribed trailer contains one conserved segment. Received: 29 May 1998; in revised form: 3 August 1998 / Accepted: 18 August 1998     

Genetic immobilization of cellulase on the cell surface of Saccharomyces cerevisiae

We tried genetically to immobilize cellulase protein on the cell surface of the yeast Saccharomyces cerevisiae in its active form. A cDNA encoding FI-carboxymethylcellulase (CMCase) of the fungus Aspergillus aculeatus, with its secretion signal peptide, was fused with the gene encoding the C-terminal half (320 amino acid residues from the C terminus) of yeast α-agglutinin, a protein involved in mating and covalently anchored to the cell wall. The plasmid constructed containing this fusion gene was introduced into S. cerevisiae and expressed under the control of the glyceraldehyde-3-phosphate dehydrogenase promoter from S. cerevisiae. The CMCase activity was detected in the cell pellet fraction. The CMCase protein was solubilized from the cell wall fraction by glucanase treatment but not by sodium dodecyl sulphate treatment, indicating the covalent binding of the fusion protein to the cell wall. The appearance of the fused protein on the cell surface was further confirmed by immunofluorescence microscopy and immunoelectron microscopy. These results proved that the CMCase was anchored on the cell wall in its active form. Received: 19 March 1997 / Received revision: 19 May 1997 / Accepted: 1 June 1997     

Streptococcal Opacity Factor: A Family of Bifunctional Proteins with Lipoproteinase and Fibronectin-Binding Activities

The serum opacity factor (SOF) of Streptococcus pyogenes is a type-specific lipoproteinase of unknown biological significance. We have sequenced the sof gene and characterized the corresponding SOF protein from a strain of type M63. It was found that sof63 is related to sof22 and that, similar to SOF22 [25], SOF63 binds fibronectin. Moreover, we demonstrate opacity factor activity in a Streptococcus dysgalactiae fibronectin-binding protein FnBA that is structurally related to the SOF proteins of S. pyogenes. Sequence analysis of these three SOF proteins showed a unique periodical pattern of conserved and variable regions. The enzymatically active part of SOF63 was localized to the fragment corresponding to the entire set of conserved and variable sequences, while for fibronectin-binding a single repeat in the C terminal part of the protein was sufficient. The results show that streptococcal SOF proteins form a novel family of bifunctional proteins with lipoproteinase and fibronectin-binding activities. Received: 7 June 1999 / Accepted: 5 October 1999     

Production of bioactive,SUMO-modified,and native-like TNF-α of the rhesus monkey, <Emphasis Type="Italic">Macaca mulatta</Emphasis>, in <Emphasis Type="Italic">Escherichia coli</Emphasis>

Biotechnologically produced tumor necrosis factor alpha (TNF-α) neutralizing agents have proven efficient in patients suffering from disparate autoimmune diseases. The rhesus monkey (Macaca mulatta) could be developed as a model for human autoimmune disease. Consequently, a large amount of M. mulatta TNF-α (mmTNFα) is required to further understand TNF-α-related pathogenesis and evaluate novel human TNF-α (hTNFα) neutralizing agents. We therefore attempted to express mmTNFα by using a small ubiquitin-like modifier (SUMO) fusion system. The synthetic gene, encoding the fusion protein SUMO-mmTNFα, was inserted into a pQE30 plasmid and was transformed into Escherichia coli M15. The fusion protein was expressed as both soluble and insoluble protein in E. coli. Approximately 10–12 mg of SUMO–mmTNFα was obtained from the soluble fraction of 1 L of bacterial culture. Cleavage of the fusion protein with SUMO protease produced native-like mmTNFα. Both native-like and SUMO-modified mmTNFα formed functional trimers and showed excellent cytotoxicity (ED₅₀, 0.05–0.1 ng/ml) in standard L929 cells. In addition, SUMO–mmTNFα and mmTNFα also exhibited cytotoxicity in human cancer cell types, such as, breast, lung, and liver cancer cells. The hTNFα neutralizing agents, including soluble receptors of hTNFα and antibodies against hTNFα, interacted with the mmTNFα. These results demonstrate that the bioactive mmTNFα produced with the SUMO fusion system is useful for further research, especially for the in vitro preclinical evaluation of biological hTNFα neutralizing agents.     

Characterization of an Alanine Racemase Gene from Lactobacillus reuteri

An alanine racemase gene from Lb. reuteri was cloned by using degenerate oligonucleotides corresponding to conserved regions derived from several bacterial alanine racemases. The protein is 375αα in length and shows 63.6% homology to the Lb. plantarum alanine racemase. Unlike the single alanine racemase activity found in Lb. plantarum, deletion of the Lb. reuteri alanine racemase reveals a second activity, which is inhibited by β-chloro-D-alanine. Received: 26 June 2001 / Accepted: 30 July 2001     

Identification of the nucleotide substitution that generates the fourth polymorphic site in human deoxyribonuclease I (DNase I)

In addition to the three polymorphic sites responsible for protein polymorphism, a new polymorphic site has been identified in intron 7 of the human deoxyribonuclease I (DNase I) gene. Three phenotypes were observed on single-strand conformational polymorphism analysis of a 266-bp polymerase chain reaction-amplified fragment containing exon 7 and part of intron 7 of the human DNase I gene. DNA sequencing analysis demonstrated that a C-G substitution occurred at position 1978 in intron 7. This substitution was confirmed by restriction fragment length polymorphism analysis, since a new Msp1 site is created by the substitution. Population and family studies showed that the inheritance of the genotypes for DNase I C1978G polymorphism is controlled by two codominant alleles, tentatively designated DNASE1*1978C and *1978G. The gene frequencies in a Japanese population were significantly different from those in a Caucasian (German) population. The C1978G polymorphism is in linkage disequilibrium with the common DNase I protein phenotypes 1, 1–2, and 2. Received: 20 March 1996 / Revised: 14 May 1996     

Inhibition of Streptococcus pyogenes Biofilm Formation by Coral-Associated Actinomycetes

Streptococcus pyogenes biofilms tend to exhibit significant tolerance to antimicrobials during infections. We screened coral-associated actinomycetes (CAA) for antibiofilm activity against different biofilm forming M serotype of Streptococcus pyogenes. Actinomycetes isolated from the mucus of the coral Acropora digitifera were screened for antibiofilm activity against S. pyogenes biofilms wherein several isolates clearly demonstrated antibiofilm activity. The biofilm inhibitory concentrations (BICs) and the sub-BICs (1/2 and 1/4 BIC) of the extracts significantly prevented biofilm formation up to 60–80%. The extract of Streptomyces akiyoshinensis (A3) displayed efficient antibiofilm activity against all the biofilm forming M serotypes. All the five extracts efficiently reduced the cell surface hydrophobicity (a crucial factor for biofilm formation in S. pyogenes) of three M types and thus may inhibit biofilm formation. CAA represent an interesting source of marine invertebrates-derived antibiofilm agents in the development of new strategies to combat Streptococcal biofilms.     

New solvent-producing Clostridium sp. strains, hydrolyzing a wide range of polysaccharides, are closely related to Clostridium butyricum

Thirteen new Clostridium strains, previously isolated from soil and found to produce high amounts of solvents from glucose, hydrolyzed a great variety of α- and β-glycans, including raw starch, xylan, pectin, inulin and cellulose. The sequences of the PCR-amplified DNA fragments containing the variable 3′ part of one of the 16S rRNA genes were 99.5% identical. The macrorestriction pattern of two endonucleolytic digests of chromosomal DNA in the pulsed-field gel electrophoresis (PFGE) confirmed their high homogeneity on the DNA level. The complete 16S rRNA gene sequence of three selected strains was 99.8% identical to the 16S rRNA gene sequence from Clostridium butyricum and separates them from C. acetobutylicum. To the closely related four species of solventogenic clostridia a new group of strains has to be added, which has a great potential for the direct fermentation of biomass. Journal of Industrial Microbiology & Biotechnology (2001) 27, 329–335. Received 12 September 2000/ Accepted in revised form 25 July 2001     

Ancient Origin of Human Complement Factor H

We studied the evolutionary history of two homologous proteins of the human complement system, factor H (FH) and the α chain of the C4b binding protein (C4bpα), and included in this study the related proteins from the barred sand bass (P. nebulifer) and the nematode C. elegans. Phylogenetic trees inferred from individual short consensus repeats (SCRs) and divergence among repeats from different genes suggest that human FH has a much closer evolutionary relationship to putative complement components from P. nebulifer and C. elegans than does the C4bpα. This indicates that a member of the alternative pathway of the complement system (FH) has an ancient origin, while a homologous member of the classical pathway (C4bpα) appeared later in evolutionary history as a result of gene duplication. The ancient evolutionary position of FH is in agreement with the suggestion that the alternative pathway of the complement system is older than the classical pathway. Phylogenetic analysis also shows that the sand bass cofactor protein SBP1 and cofactor related protein SBCRP-1 have diverged very recently. Received: 1 December 1997 / Accepted: 3 June 1998     

Cloning of α-amylase gene from Schwanniomyces occidentalis and expression in Saccharomyces cerevisiae

The cloning of α-amylase gene ofS. occidentalis and the construction of starch digestible strain of yeast,S. cerevisiae AS. 2. 1364 with ethanol-tolerance and without auxotrophic markers used in fermentation industry were studied. The yeast/E.coli shuttle plasmid YCEp1 partial library ofS. occidentalis DNA was constructed and α-amylase gene was screened in S.cerevisiae by amylolytic activity. Several transformants with amylolysis were obtained and one of the fusion plasmids had an about 5.0 kb inserted DNA fragment, containing the upstream and downstream sequences of α-amylase gene fromS. occidentalis. It was further confirmed by PCR and sequence determination that this 5.0 kb DNA fragment contains the whole coding sequence of α-amylase. The amylolytic test showed that when this transformant was incubated on plate of YPDS medium containing 1 % glum and 1 % starch at 30°C for 48 h starch degradation zones could be visualized by staining with iodine vapour. α-amylase activity of the culture filtratate is 740–780 mU/mL and PAGE shows that the yeast harboring fusion plasmids efficiently secreted α-amylase into the medium, and the amount of the recombinant α-amylase is more than 12% of the total proteins in the culture filtrate. These results showed that α-amylase gene can be highly expressed and efficiently secreted inS. cerevisiae AS. 2.1364, and the promotor and the terminator of α-amylase gene fromS. occidentalis work well inS. cercvisiac AS. 2.1364.     

Tissue specificity and expression level of gusA under rolD, mannopine synthase and translation elongation factor 1 subunit a promoters in transgenic Gladiolus plants

Transgenic plants of Gladiolus cv. Jenny Lee were developed that contain the bargusA fusion gene under either the mannopine synthase 2 (mas2), translation elongation factor 1 subunit α (EF-1α), rolD, or the cauliflower mosaic virus 35S (CaMV 35S) promoters. The relative level of gusA expression in leaves of five to ten independently transformed, in-vitro-grown plants representing each promoter was similar for transgenic plants containing the rolD and CaMV 35S promoter and 2.0-fold and 3.3-fold higher than the level for the mas2 and EF-1α promoters, respectively. The maximum level of gusA specific activity by leaves was 135–173 nmol 4-methylumbelliferone (4-MU)/h per milligram protein for plants containing either CaMV 35S or rolD as compared to only 27–38 nmol 4-MU/h per milligram protein for plants with either mas2 or EF-1α. Histochemical staining confirmed the relatively high level of gusA expression throughout the length of the older, 6-cm-long leaves of plants that contained bargusA under rolD, whereas gusA expression was infrequently observed throughout the older leaves of plants containing either the mas2 or EF-1α promoters. In contrast to the older leaves, staining showed that strong gusA expression was frequently observed throughout young leaves of plants with either the mas2, EF-1α, or rolD promoters. Roots of plants with the rolD and EF-1α promoters showed strong gusA expression specifically in 93% and 68%, respectively, of the root tips. Roots of the plants with the mas2 promoter showed strong gusA expression throughout the entire length of the root. Received: 7 May 1998 / Revision received: 1 December 1998 / Accepted: 17 December 1998     

An Examination of the Differential Sensitivity to Ketolide Antibiotics in <Emphasis Type="Italic">ermB</Emphasis> Strains of <Emphasis Type="Italic">Streptococcus pyogenes</Emphasis> and <Emphasis Type="Italic">Streptococcus pneumoniae</Emphasis>

Several reports in the literature have described a differential sensitivity to ketolide antibiotics in ermB strains of Streptococcus pyogenes and Streptococcus pneumoniae resistant to erythromycin. Strains of S. pyogenes and S. pneumoniae carrying different erm gene alleles were examined for their susceptibility to the ketolide antibiotics cethromycin (ABT-773) and telithromycin. The effect of the antibiotics on cell growth and viability was assessed as were effects on protein synthesis and 50S ribosomal subunit formation. The susceptibility of wild-type strains of both organisms was compared with effects in strains containing the ermA and ermB methyltransferase genes. A wild-type antibiotic-susceptible strain of S. pyogenes was comparable to an ermA strain of the organism in its ketolide sensitivity, with IC₅₀ values for 50% inhibition of protein synthesis and 50S ribosomal subunit formation of 10 ng/mL for cethromycin and 16 ng/mL for telithromycin. An S. pneumoniae strain with the ermB gene and an S. pyogenes strain with the ermA gene were also similar in their sensitivity to ketolide inhibition. IC₅₀ values for inhibition of translation and subunit formation in S. pneumoniae (ermB) were 30 ng/mL and 55 ng/mL and for the ermA strain of S. pyogenes they were 15 ng/mL and 35 ng/mL respectively. By contrast, an S. pyogenes ermB strain was significantly more resistant to both ketolides, with IC₅₀ values for inhibition of 50S synthesis of 215 and 380 ng/mL for the two ketolides. Experiments were conducted to examine ribosome synthesis and translational activity in the two ermB strains at intervals during growth in the presence of each antibiotic. Cell viability and 50S subunit formation were dramatically reduced in the S. pneumoniae strain during continued growth with either drug. By contrast, the ketolides had little effect on the S. pyogenes strain growing with the antibiotics. The results indicate that ketolides have a reduced inhibitory effect on translation and 50S subunit synthesis in S. pyogenes with the ermB gene compared with the other strains examined.     

Isolation and characterization of the fission yeast gene rpa42+, which encodes a subunit shared by RNA polymerases I and III

Eukaryotic RNA polymerases I and III share two distinct α-related subunits that show limited homology to the α subunit of Escherichia coli RNA polymerase, which forms a homodimer to nucleate the assembly of prokaryotic RNA polymerase. To gain insight into the functions of α-related subunits in eukaryotes, we have previously identified the α-related small subunit RPA17 of RNA polymerase I (and III) in Schizosaccharomyces pombe, and have shown that it is a functional homolog of Saccharomyces cerevisiae AC19. In an extension of that study, we have now isolated and characterized rpa42 ⁺, which encodes the α-related large subunit RPA42 of S. pombe RNA polymerase I, by virtue of the fact that its product interacts with RPA17 in the yeast two-hybrid system. We have found that rpa42 ⁺ encodes a polypeptide with an apparent molecular mass of 42 kDa, which shows 58% identity to the AC40 subunit shared by RNA polymerases I and III in S. cerevisiae. Furthermore, we have shown that rpa42 ⁺ complements a temperature-sensitive mutation in RPC40 the gene that encodes AC40 in S. cerevisiae and which is essential for cell growth. Finally, we have shown that neither RPA42 nor RPA17 can self-associate. These results provide evidence that the two distinct α-related subunits, RPA42 and RPA17, of RNA polymerases I and III are functionally conserved between S. pombe and S. cerevisiae, and suggest that heterodimer formation between them is essential for the assembly of RNA polymerases I and III in eukaryotes. Received: 20 April 1999 / Accepted: 26 July 1999