[Search for destruction factors of bacterial biofilms: comparison of phage properties in a group of Pseudomonas putida bacteriophages and specificity of their halo-formation products]

Comparison of Pseudomonas putida group of phages attributed to five species (af, phi15, phi27, phi2F, and pf16) with their common property of halo-formation (formation of lightening zones) around phage plaques was conducted. The halo around phage plaques appears as a result of reduction or disappearance of bacterial polysaccharide capsules. The concentration of viable bacteria remains unchanged within the halo. A comparison of specificities of halo-formation products from various phages was conducted by a simple method. These products were shown to be highly specific and inactive on other species of pseudomonads. Phage-resistant P. putida mutants scored with respect to various phages, which lost phage adsorption ability, were tolerant to the effect of halo-formation products in most cases. Apparently, the capsular polysaccharides, which serve as a substrate for depolymerases and are the primary phage receptors, may be often lost. Results of partial sequencing of the af phage genome revealed an open reading frame that encodes the enzyme transglycosylase similar rather to transglycosylases of oligotrophic bacteria belonging to different species than to lysozymes of other phages. Possibly, it is a polyfunctional enzyme combining functions of lysozyme and an enzyme that executes the penetration of phage particle across extracellular slime and capsule.

Homotypic interactions among bacteriophage phiKMV early proteins

Little is known about the bacteriophage proteins expressed immediately after infection of the host cell. Most of these early proteins are probably involved in bacteriophage-host interactions redirecting the bacterial metabolism to phage production. Interaction analysis of the first 16 phiKMV gene products (gp) identified homotypic interactions of gp7, gp9 and gp15. Two related yeast two-hybrid procedures, a matrix and a minilibrary approach, were applied to detect protein-protein interactions. A two-step selection procedure enabled drastic reduction of the background. Interactions were confirmed by drop tests. Multimerization of gp15 is consistent with its putative function as a DNA helicase involved in DNA replication. Homotypic interaction of gp7 and gp9 suggests they function as dimers or multimers. The absence of heterotypic interactions among early phiKMV proteins hints at their functional independence from other early phage proteins and their involvement in phage-host interactions that are important for creating optimal conditions for phage propagation. Besides, these results demonstrate the compatibility of phiKMV early gene products with the yeast two-hybrid system. Therefore, they are promising candidates to screen for interactions with host proteins.

Stability analysis of the bacteriophage ϕKMV lysin gp36C and its putative role during infection

The kinetic, thermodynamic and structural stability of gp36C, the virion-associated peptidoglycan hydrolase domain of bacteriophage phiKMV, is analyzed. Recombinant gp36C is highly thermoresistant (k = 0.595 h(-1) at 95 degrees C), but not thermostable (T(m) = 50.2 degrees C, DeltaH(cal) = 6.86 x 10(4) cal mol(-1)). However, aggregation influences kinetic stability in an unusual manner since aggregation is more pronounced at 55 degrees C than at higher temperatures. Furthermore, gp36C reversibly unfolds in a two-state endothermic transition, and circular dichroism analysis shows that gp36C almost completely refolds after a 3-h heat treatment at 85 degrees C. These properties are in agreement with gp36C being part of the extensible tail which is ejected in an unfolded state during phage infection.

Characterization of the Bacteriophage ΦKMV DNA Ligase

Gene 17 product (gp17) of the Pseudomonas aeruginosa-infecting bacteriophage phiKMV shows in silico similarity to T7 DNA ligase. In a semi-quantitative activity assay, it is shown that gp17 is a functional, ATP-dependent DNA ligase, in spite of some structural differences related to DNA-binding properties). Enzymatic activity of His6-based purified expression product was optimised (4 degrees C at 24h for sticky end double-stranded DNA fragments) and estimated at 0.5 Weiss U/microg.

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.

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.

Molecular identification and chromosomal localization of genes encoding Triticum aestivum xylanase inhibitor I-like proteins in cereals

TAXI ( Triticum aestivum xylanase inhibitor) proteins are present in wheat flour and are known to inhibit glycosyl hydrolase family 11 endoxylanases, enzymes which are commonly applied in grain processing. Here, we describe the PCR-based molecular identification of genes encoding endoxylanase inhibitors HVXI and SCXI, the TAXI-like proteins from barley ( Hordeum vulgare) and rye ( Secale cereale) respectively. The HVXI coding sequence encodes a mature protein of 384 amino acids preceded by a 19 amino acid long signal sequence. SCXI-II/III has an open reading frame encoding a signal peptide of 21 amino acids and a mature protein of 375 amino acids. As for TAXI-I, no introns were detected in the untranslated regions and coding sequences identified. These newly identified sequences allowed us to perform a multiple sequence alignment with TAXI-I and similar proteins. Rice TAXI-type proteins clustered together with the cereal endoxylanase inhibitors. Dicotyledonous proteins with sequence similarity to TAXI-I, including the tomato xyloglucan-specific endoglucanase inhibiting protein, formed a different clade. The TAXI-type proteins may hence be part of a superfamily of proteins all involved in plant responses to biotic or abiotic stress and for which a function as glycosyl hydrolase inhibitors can be suggested. The chromosomal localization of the TAXI-I gene identified on wheat chromosome 3B, of the SCXI-II/III gene identified on rye chromosome 6R, and the presence of a cluster of TAXI-like genes on rice chromosome 1, allowed us to assign the location of TAXI-like genes to the wheat-rye translocation area 3BL/6RL characterized by RFLP markers XGlb33 and Xpsr454 and isozyme Est-5. In rice, RFLP marker C1310S corresponds to a TAXI-like protein encoding sequence.

Gene content and density in banana ( Musa acuminata) as revealed by genomic sequencing of BAC clones

The complete sequence of Musa acuminata bacterial artificial chromosome (BAC) clones is presented and, consequently, the first analysis of the banana genome organization. One clone (MuH9) is 82,723 bp long with an overall G+C content of 38.2%. Twelve putative protein-coding sequences were identified, representing a gene density of one per 6.9 kb, which is slightly less than that previously reported for Arabidopsis but similar to rice. One coding sequence was identified as a partial M. acuminata malate synthase, while the remaining sequences showed a similarity to predicted or hypothetical proteins identified in genome sequence data. A second BAC clone (MuG9) is 73,268 bp long with an overall G+C content of 38.5%. Only seven putative coding regions were discovered, representing a gene density of only one gene per 10.5 kb, which is strikingly lower than that of the first BAC. One coding sequence showed significant homology to the soybean ribonucleotide reductase (large subunit). A transition point between coding regions and repeated sequences was found at approximately 45 kb, separating the coding upstream BAC end from its downstream end that mainly contained transposon-like sequences and regions similar to known repetitive sequences of M. acuminata. This gene organization resembles Gramineae genome sequences, where genes are clustered in gene-rich regions separated by gene-poor DNA containing abundant transposons.

Influence of maternal antibodies on Chlamydophila psittaci-specific immune responses in turkeys elicited by naked DNA

Plasmid DNA (pcDNA1::MOMP D) expressing the major outer membrane protein (MOMP) of an avian Chlamydophila psittaci serovar D strain was tested for its ability to induce protective immunity against C. psittaci challenge in the presence of maternal antibodies. A combined parenteral (intramuscular injection) and mucosal route (DNA drops administered to the nares) of DNA inoculation was used. Following pcDNA1::MOMP vaccination, both T helper and B cell memory were primed. However, high maternal antibodies titres affected the induction of vaccine-specific antibody responses as assessed by MOMP-specific antibody levels in enzyme-linked immunosorbent assay (ELISA). Cell-mediated immunity was unaltered as demonstrated by the significantly heightened proliferative responses of peripheral blood lymphocytes (PBL) following vaccination. DNA vaccination could significantly reduce clinical symptoms, pharyngeal and cloacal excretion as well as Chlamydophila replication, even in the presence of maternal antibodies.

PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes

MOTIVATION

In silico genome analysis of bacteriophage genomes focuses mainly on gene discovery and functional assignment. The search for regulatory elements contained within these genome sequences is often based on prior knowledge of other genomic elements or on learning algorithms of experimentally determined data, potentially leading to a biased prediction output. The PHage In silico Regulatory Elements (PHIRE) program is a standalone program in Visual Basic. It performs an algorithmic string-based search on bacteriophage genome sequences to uncover and extract subsequence alignments hinting at regulatory elements contained within these genomes, in a deterministic manner without any prior experimental or predictive knowledge.

RESULTS

The PHIRE program was tested on known phage genomes with experimentally verified regulatory elements. PHIRE was able to extract phage regulatory sequences correctly for bacteriophages T7, T3, YeO3-12 and lambda, based solely on the genome sequence. For 11 bacteriophages, new predictions of conserved phage-specific putative regulatory elements were made, further corroborating this approach.

AVAILABILITY

http://www.agr.kuleuven.ac.be/logt/PHIRE.htm. Freely available for academic use. Commercial users should contact the corresponding author.

Molecular characterization and phylogenetic utility of the rDNA external transcribed spacer region in Stylosanthes (Fabaceae)

Supplementary Material The nucleotide sequence of the ribosomal external transcribed spacer (ETS) region of Stylosanthes mexicana was determined and used to evaluate its potential for examination of intra- and inter-specific relationships in Stylosanthes, as compared to the use of the internal transcribed spacer (ITS) region. The entire ETS region comprises 1,145 bp and is composed of a region of non-repetitive sequences consisting of three subregions with organizational and nucleotide-sequence conservation, and a triplicated segment of about 100 bp. A primer designed in the second conserved subregion allowed us to amplify and sequence directly the 3' part (423-431 bp) of the ETS from 22 genotypes of 12 representative Stylosanthes species that were previously used in phylogenetic analysis of the genus. The study revealed that the right-hand part of Stylosanthes ETS contains approximately twice as much variable and informative characters than the ITS. Moreover, pairwise sequence-divergence values are twice as high, on average, when compared to the ITS. The ITS and ETS datasets are consistent in phylogenetic reconstruction of Stylosanthes, and combined parsimony analysis resulted in a strict consensus tree that is better resolved and generally better supported than trees obtained from separate analysis of the spacer regions.

Missing links in the divergence of Chlamydophila abortus from Chlamydophila psittaci

Pathological and serological evidence and DNA-DNA reassociation data indicate that Chlamydophila psittaci and Chlamydophila abortus are separate species. C. psittaci causes avian systemic disease and C. abortus causes abortion. Both previously belonged to Chlamydia psittaci are associated with zoonotic and enzootic outbreaks. Genetic studies suggest that they are closely related and because of the recent availability of diverse C. psittaci strains and comparative data for several genes, it was possible to explore this relationship. The parrot C. psittaci strain 84/2334 was found to have DNA sequences that were identical to an extrachromosomal plasmid in duck C. psittaci strain N352, to rnpB in strain R54 from a brown skua and to the rrn intergenic spacer in parakeet strain Prk/Daruma (from Germany, Antarctica and Japan, respectively). Analysis of ompA and the rrn spacer revealed progressive diversification of the strains, with 84/2334 resembling what might have been a recent ancestor of C. abortus. Another C. psittaci strain (VS225) showed evidence of having undergone convergent evolution towards the C. abortus-like genotype, whereas strain R54 diverged independently. For the first time, these studies link C. abortus in an evolutionary context to the C. psittaci lineage. It has been concluded that C. abortus diverged from C. psittaci, and so strain R54 was designated a C. psittaci strain. It is recommended that characterization of C. psittaci and C. abortus strains should utilize more than a single method and more than a single gene.

Regulation of inhibin alpha- and beta(A)-subunit messenger ribonucleic acid levels by gonadotropins and IGF-I in cultured chicken granulosa cells

A quantitative competitive reverse transcription polymerase chain reaction assay (QC RT-PCR) for quantifying the absolute levels of the expression of inhibin alpha- and beta(A)-subunits in chicken granulosa cells showed that these subunits are expressed in different amounts depending on follicular maturation. The present study determined the regulation of the expression of these subunits. The individual effect of different doses of IGF-I, LH or FSH (1-100 ng/ml) or the combination of IGF-I with either LH or FSH at different concentrations, on the expression of inhibin alpha- and beta(A)-subunit was determined on cultured granulosa cells of F(1) and the combined F(4)+F(5) follicle. Cells were cultured for 48 h in 6-well plates with or without added hormones. Culture medium was discarded, cells were washed and total RNA was extracted from the cells. Five hundred nanograms of total RNA was reverse transcribed using specific primers and coamplified with an internal standard, as described previously, to determine expression level in the cells. IGF-I, LH, and FSH enhanced the inhibin alpha-subunit mRNA levels in a dose dependent manner in both F(1) and the combined F(4)+F(5) whereas inhibin beta(A)-subunit was not affected. The effects of FSH, LH were more expressed in F(1) follicles compared to F(4)+F(5) on the alpha-subunit. The addition of IGF-I and either LH or FSH during the culture period significantly increased the stimulatory effects of both LH and FSH on the expression of inhibin alpha-subunit in F(1) follicles but had no significant effect on the inhibin beta(A)-subunit. The results suggest that the changing expression levels of inhibin alpha-subunit during follicular development are the result of the regulatory effect of the interaction between IGF-I and the gonadotropins and that the regulation of this subunit may be the main factor for the regulation of the protein inhibin levels. Other factors may be also implicated in the changing expression levels of the beta(A)-subunit.

Chlamydophila psittaci DNA vaccination in turkeys in the presence of maternal antibodies

Plasmid DNA (pcDNA1::MOMP D) expressing the major outer membrane protein of an avian Chlamydophila psittaci serovar D strain was tested for its ability to induce protective immunity against Chlamydophila psittaci challenge in the presence of maternal antibodies. A combined parenteral (intramuscular injection) and mucosal route (DNA drops administered to the nares) of DNA inoculation was used. Only placebo-vaccinated turkeys showed a primary response following challenge, although DNA vaccination didn't generate high antibody titres. Following pcDNA::MOMP vaccination, both T-helper and B-cell memory were primed. However, high maternal antibodies titres affected the induction of vaccine-specific antibody responses as assessed by MOMP-specific antibody levels in ELISA. Cell-mediated immunity was unaltered as demonstrated by the significantly heightened proliferative responses of peripheral blood lymphocytes following vaccination. DNA vaccination could significantly reduce clinical symptoms, pharyngeal and cloacal excretion as well as chlamydophila replication, even in the presence of maternal antibodies.

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.

Genetic immunization for Chlamydia psittaci

Plasmid DNA expressing the major outer membrane protein (MOMP) of an avian Chlamydia psittaci serovar A strain, has been tested for its ability to raise an immune response and induce protection against challenge with the same serovar. A combined parenteral (intramuscular injection) and mucosal route (DNA drops administered to the nares) of DNA inoculation was compared to gene gun-based immunization. The gene gun delivery of pcDNA1/MOMP as well as the intramuscular-intranasal DNA delivery primed both T-helper and B-cell memory although rMOMP-expressing cells did not induce high antibody responses. Evidence for the priming of the memory was provided by the fact that the pcDNA1/MOMP inoculations raised antibodies belonging to the IgG and not IgM isotype. However, in response to challenge only 5 out of 15 vaccinated turkeys showed four fold increases in serum IgG after challenge. By contrast, evidence for the priming of T-cell memory in response to challenge was found in all vaccinated turkeys as shown by the significantly heightened proliferative responses of peripheral blood lymphocytes following vaccination. Both immunization methods produced similar serological and lymphocyte proliferative responses. Notwithstanding the immunization method, a significant level of protection was observed in all pcDNA1/MOMP immunized turkeys. The efficacy of MOMP-based DNA vaccination as a means of preventing severe clinical signs, lesions and chlamydia excretion in a turkey model of Chlamydia psittaci infection was demonstrated.

The specific isolation of complete 5S rDNA units from chromosome 1A of hexaploid, tetraploid, and diploid wheat species using PCR with head-to-head oriented primers

The presence of 5S rDNA units on chromosome 1A of Triticum aestivum was shown by the development of a specific PCR test, using head-to-head oriented primers. This primer set allowed the amplification of complete 5S DNA units and was used to isolate SS-Rrna-A1 sequences from polyploid and diploid wheat species. Multiple-alignment and parsimony analyses of the 132 sequences divided the sequences into four types. The isolates from T. aestivum and the tetraploid species (T. dicoccoides, T. dicoccum, T durum, T. araraticum, and T timopheevi) were all of one type, which was shown to be closely related to the type mainly characteristic for T. urartu. The other two types were isolated exclusively from the diploid species T. monococcum, T aegilopoides, T. thaoudar, and T. sinskajae and the hexaploid species T. zhukovski. Triticum monococcum was the only species for which representatives of each of the four sequence types were found to be present. Further, we discuss the possible multicluster arrangement of the 5S-Rrna-A1 array.

The specific isolation of complete 5S rDNA units from chromosome 1A of hexaploid, tetraploid, and diploid wheat species using PCR with head-to-head oriented primers

The presence of 5S rDNA units on chromosome 1A of Triticum aestivum was shown by the development of a specific PCR test, using head-to-head oriented primers. This primer set allowed the amplification of complete 5S DNA units and was used to isolate 5S-Rrna-A1 sequences from polyploid and diploid wheat species. Multiple-alignment and parsimony analyses of the 132 sequences divided the sequences into four types. The isolates from T. aestivum and the tetraploid species (T. dicoccoides, T. dicoccum, T. durum, T. araraticum, and T. timopheevi) were all of one type, which was shown to be closely related to the type mainly characteristic for T. urartu. The other two types were isolated exclusively from the diploid species T. monococcum, T. aegilopoides, T. thaoudar, and T. sinskajae and the hexaploid species T. zhukovski. Triticum monococcum was the only species for which representatives of each of the four sequence types were found to be present. Further, we discuss the possible multicluster arrangement of the 5S-Rrna-A1 array.Key words: Triticum, A genome, PCR markers, 5S ribosomal RNA locus.

Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thaliana

The nucleotide sequence was determined for a 340-kb segment of rice chromosome 2, revealing 56 putative protein-coding genes. This represents a density of one gene per 6.1 kb, which is higher than was reported for a previously sequenced segment of the rice genome. Sixteen of the putative genes were supported by matches to ESTs. The predicted products of 29 of the putative genes showed similarity to known proteins, and a further 17 genes showed similarity only to predicted or hypothetical proteins identified in genome sequence data. The region contains a few transposable elements: one retrotransposon, and one transposon. The segment of the rice genome studied had previously been identified as representing a part of rice chromosome 2 that may be homologous to a segment of Arabidopsis chromosome 4. We confirmed the conservation of gene content and order between the two genome segments. In addition, we identified a further four segments of the Arabidopsis genome that contain conserved gene content and order. In total, 22 of the 56 genes identified in the rice genome segment were represented in this set of Arabidopsis genome segments, with at least five genes present, in conserved order, in each segment. These data are consistent with the hypothesis that the Arabidopsis genome has undergone multiple duplication events. Our results demonstrate that conservation of the genome microstructure can be identified even between monocot and dicot species. However, the frequent occurrence of duplication, and subsequent microstructure divergence, within plant genomes may necessitate the integration of subsets of genes present in multiple redundant segments to deduce evolutionary relationships and identify orthologous genes.

Developmental expression of activin/inhibin alpha- and beta(A)-subunit genes in the gonads of male and female chick embryos

The expression of inhibin alpha- and beta(A)-subunits was investigated in gonads of male and female chick embryos during the last week of their 21-day incubation period. Fertilized Hisex brown laying hen eggs were incubated at 37.8 +/- 0.2 degrees and 60% relative humidity in an automatic forced-draft incubator with constant lighting. Embryos were killed after 14, 18, and 21 days of incubation, sexed by macroscopical inspection of the gonadal phenotype, and further dissected to obtain the gonads. Total RNA was isolated using the ultraspec RNA method. The expression of alpha- and beta(A)-subunits was evaluated by competitive RT-PCR. Significant differences were found within and between sexes in the expression of the alpha- and beta(A)-subunits. The level of the alpha-subunit in the testis was about 23-fold higher than that in the ovary at all ages. Testicular content of inhibin alpha mRNA levels was similar at days 14 and 18 but declined significantly at day 21 of incubation, whereas no significant differences were observed between the three age groups in the ovary. Testicular and ovarian inhibin beta(A)-subunit increased significantly from day 14 to day 18 followed by a significant decline before hatch. However, inhibin beta(A) level at day 14 was significantly higher in the ovary than in the testis. At days 18 and 21, there were no differences in the levels of the inhibin beta(A) in the sexes. The expression of inhibin beta(A)-subunit in the ovary was significantly higher than that of the alpha-subunit at all ages. In the testis, however, the expression of the beta(A)-subunit was higher at days 18 and 21 than at day 14. The sex difference in gonadal inhibin subunits expression suggests differential roles of inhibin/activin in the development of the chicken gonads. The changing level of expression during incubation also suggests changing biological roles within sexes.

Protection of turkeys against Chlamydophila psittaci challenge by parenteral and mucosal inoculations and the effect of turkey interferon-gamma on genetic immunization

Plasmid DNA (pcDNA1::MOMP A) expressing the major outer membrane protein of an avian Chlamydophila psittaci serovar A strain was tested for its ability to induce protective immunity against challenge with the same C. psittaci serovar. A combined parenteral (intramuscular injection) and mucosal route (DNA drops administered to the nares) of DNA inoculation was compared to three other, different routes of administration (intramuscular inoculation, DNA drops administered to the nares and aerosol immunization). In addition, the effect of turkey interferon gamma (tIFN-gamma) on intramuscular immunization was evaluated by co-expressing pCIneo::tIFN-gamma. A significant level of protection was observed in turkeys immunized via the combined parenteral/mucosal route, the intramuscular route or by aerosol. Severe clinical signs and lesions were observed in the non-vaccinated control groups, in 80% of turkeys inoculated with a mixture of pcDNA1::MOMP A and pCIneo::tIFN-gamma, and in 60% of turkeys vaccinated with DNA drops administered to the nares. The use of MOMP-based DNA vaccination as a means of preventing severe clinical signs and lesions in a turkey model of C. psittaci infection was demonstrated, as was down-regulation of the immune response by co-expression of tIFN-gamma.

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.

The fortuitous cloning of retroelement-like sequences from wheat and rye as by-products of a specific polymerase chain reaction

Cloning of by-products of a specific PCR reaction, directed to the Em genes of wheat and rye, has resulted in the identification of ten sequences with homology to the known Tyl-copia-like retroelements WIS 2-1A from wheat and BARE-1 from barley. These sequences were amplified by only one of the primers due to the presence of an inverted repeat. Nine sequences are ca. 740 bp long and contain part of the left LTR, the adjacent primer-binding site and part of the leader sequence, whereas one shorter sequence (535 bp) consists of part of the leader sequence only. The dendrogram, constructed from the multiple sequence alignment, classified the isolated sequences into two narrowly related groups that belong to the WIS-2 family of cereal retroelements.

Molecular characterization and classification of Stylosanthes mexicana, S. macrocarpa, S. seabrana and S. fruticosa by DNA sequence analysis of two chloroplast regions

The trnL (UAA) intron and trnL (UAA) - trnF (GAA) intergenic spacer region from the diploid species Stylosanthes mexicana, S. macrocarpa and S. seabrana and the tetraploid species S. fruticosa were amplified by polymerase chain reaction and subjected to direct DNA sequencing. Comparison of these chloroplast regions with previously determined DNA sequences of 19 Stylosanthes species revealed a close relationship with a clade containing the diploid species S. hamata, S. calcicola, and the tetraploid species S. scabra. The results were used to infer relationships between the diploid species of this clade, in relation to the alloploid species S. scabra and S. fruticosa.

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.

Expression of chymotrypsin(ogen) in the thioredoxin reductase deficient mutant strain of Escherichia coli AD494(DE3) and purification via a fusion product with a hexahistidine-tail

A reliable protocol was designed for fast expression and purification of recombinant chymotrypsin(ogen). The zymogen was overexpressed in soluble form as a (His)6-fusion construct in the cytoplasm of the thioredoxin reductase deficient Escherichia coli strain AD494(DE3). This allowed purification of chymotrypsinogen in a highly selective affinity chromatography capture step using a Ni-NTA column. After activation with enterokinase, the enzymatically active chymotrypsin was purified in a polishing step using a modified soybean trypsin inhibitor agarose column. This expression system and the use of affinity chromatography for capture and polishing, offers an easier and faster route to recombinant chymotrypsin(ogen) than the previously described use of Saccharomyces cerevisiae.

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.

Turkeys are protected from infection with Chlamydia psittaci by plasmid DNA vaccination against the major outer membrane protein

Plasmid DNA expressing the major outer membrane protein (MOMP) of an avian Chlamydia psittaci serovar A strain has been tested for its ability to raise an immune response and induce protection against challenge with the same serovar. A combined parenteral (intramuscular injection) and mucosal route (DNA drops administered to the nares) of DNA inoculation was compared with gene gun-based immunization. The gene gun delivery of pcDNA1/MOMP as well as the intramuscular-intranasal DNA delivery primed both T-helper and B cell memory, although rMOMP-expressing cells did not induce high antibody responses. Evidence for the priming of the memory was provided by the fact that the pcDNA1/MOMP inoculations raised antibodies belonging to the IgG and not IgM isotype. However, in response to challenge only five out of 15 vaccinated turkeys showed four-fold increases in serum IgG after challenge. By contrast, evidence for the priming of T cell memory in response to challenge was found in all vaccinated turkeys, as shown by the significantly heightened proliferative responses of peripheral blood lymphocytes following vaccination. Both immunization methods produced similar serological and lymphocyte proliferative responses. Notwithstanding the immunization method, a significant level of protection was observed in all pcDNA1/MOMP-immunized turkeys. The efficacy of MOMP-based DNA vaccination as a means of preventing severe clinical signs, lesions and chlamydia excretion in a turkey model of C. psittaci infection was demonstrated.

Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis

The functions of many open reading frames (ORFs) identified in genome-sequencing projects are unknown. New, whole-genome approaches are required to systematically determine their function. A total of 6925 Saccharomyces cerevisiae strains were constructed, by a high-throughput strategy, each with a precise deletion of one of 2026 ORFs (more than one-third of the ORFs in the genome). Of the deleted ORFs, 17 percent were essential for viability in rich medium. The phenotypes of more than 500 deletion strains were assayed in parallel. Of the deletion strains, 40 percent showed quantitative growth defects in either rich or minimal medium.

Time resolved fluorescence and phosphorescence properties of the individual tryptophan residues of barnase: evidence for protein-protein interactions

Steady-state and time-resolved fluorescence, as well as phosphorescence measurements, were used to resolve the luminescence properties of the three individual tryptophan residues of barnase. Assignment of the fluorescence properties was performed using single-tryptophan-containing mutants and the results were compared with the information available from the study of wild-type and two-tryptophan-containing mutants (Willaert, Lowenthal, Sancho, Froeyen, Fersht, Engelborghs, Biochemistry 1992;31:711-716). The fluorescence and the phosphorescence emission of wild-type barnase is dominated by Trp35, although Trp71 has the strongest intrinsic fluorescence when present alone. Fluorescence emission of these two tryptophan residues is blue-shifted and pH-independent. The fluorescence decay parameters of Trp94 are pH-dependent, and an intramolecular collision frequency of 2 to 5 x 10(9) s(-1) between Trp94 and His18 is calculated. Fluorescence emission of Trp94 is red-shifted. Fluorescence anisotropy decay reveals the local mobility of the individual tryptophan residues and this result correlates well with their phosphorescence properties. Trp35 and Trp71 display a single phosphorescence lifetime, which reflects the rigidity of their environment. Surface Trp94 does not exhibit detectable phosphorescence emission. The existence of energy transfer between Trp71 and Trp94, as previously detected by fluorescence measurements, is also observed in the phosphorescence emission of barnase. Dynamic quenching causes the phosphorescence intensity to be protein-concentration dependent. In addition, fluorescence anisotropy shows concentration dependency, and this can be described by the formation of trimers in solution.

Protection of turkeys against Chlamydia psittaci challenge by gene gun-based DNA immunizations

Particle-mediated (Helios Gene Gun) transfer to the turkey epidermis of plasmid DNA expressing the major outer membrane protein (MOMP) of an avian Chlamydia psittaci strain was evaluated for its ability to raise an immune response and protection against challenge with the homologous strain. In turkeys, the delivery of pcDNA1/MOMP coated onto 0.6 microm gold beads was the most efficient compared to immunisations using 1.0 or 1.6 microm gold beads. The delivery of as little as 1 microg pcDNA1/MOMP coated onto 0.6 microm gold beads was efficient. Immunisation with 1.0 microm gold beads required twice more (2 microg) DNA to achieve comparable results. The use of 2 microg DNA coated onto 1.6 microm gold beads had no effects. The gene gun delivery both primed T-helper and B-cell memory although recombinant MOMP-expressing cells did not induce high-titre antibody responses. The significance of gene gun-based DNA immunisation as a means of preventing severe clinical signs, lesions and chlamydia excretion in a turkey model of Chlamydia psittaci infection was demonstrated.

Interspecific and progeny relationships in the genus Stylosanthes inferred from chloroplast DNA sequence variation

The chloroplast trnL (UAA) intron and trnL (UAA)-trnF (GAA) intergenic spacer region have been sequenced from 37 samples, 36 of which representing 19 Stylosanthes species and one from the related genus Zornia. The DNA sequences were used to study phylogenetic relationships in the tropical forage legume genus Stylosanthes, by means of parsimony analysis using the heuristic search method of the computer program PAUP. The resulting cladograms divide Stylosanthes into four separate clades. Within the clades, species are poorly resolved owing to low sequence divergence. Small intra-specific chloroplast DNA variation is observed in S. humilis, S. scabra and the species complex S. guianensis. Variation between S. humilis populations is considered to be geographically structured. The overall results agree well with previously established inter-specific relationships and provide evidence for the genetic origin of the alloploid species S. hamata, S. scabra, S. ingrata, S. sympodialis, S. subsericea, S. capitata and S. fruticosa. This understanding of evolutionary relationships in Stylosanthes, in combination with biogeographical concepts provides a way of discerning isolated habitats in Central and South America, which may therefore contribute to strategies of plant collecting.

Tryptophan microstate reshuffling upon the binding of cyclosporin A to human cyclophilin A

Human cyclophilin A (hCypA) contains one tryptophan residue at position 121 (Trp121). The fluorescence intensity of this single tryptophan residue doubles upon binding the clinically important immunosuppressant cyclosporin A (CsA). Trp121 is in close contact to the bound CsA and is well-conserved in almost all immunophilins. The enhancement of the fluorescence intensity upon binding CsA is investigated by steady-state and time-resolved fluorescence measurements. The crystal structures of hCypA and the complex hCypA-CsA are compared. Only Glu120 is strongly influenced by the binding of CsA. The distance between the indole ring and the carboxylate group doubles during complexation. The influence of Glu120 on the fluorescence properties of Trp121 was investigated by pH-titration, and by substituting glutamate into an aspartate and an alanine residue. The fluorescence measurements on the glutamate mutants reveal that the carboxylate group influences the fluorescence properties of Trp121 to a limited extent. The major effect of CsA binding, however, consists in a reshuffling of the populations of microconformations of Trp121 leading to a selective increase of the 1.5 ns lifetime component. This selection is also accompanied by a decreased polarity of the environment and an increase in the radiative rate constant.

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.

High-level expression of Chlamydia psittaci major outer membrane protein in COS cells and in skeletal muscles of turkeys

The omp1 genes encoding the major outer membrane proteins (MOMPs) of avian Chlamydia psittaci serovar A and D strains were cloned and sequenced. The nucleotide sequences of the avian C. psittaci serovar A and D MOMP genes were found to be 98.9 and 87.8% identical, respectively, to that of the avian C. psittaci serovar A strain 6BC, 84.6 and 99.8% identical to that of the avian C. psittaci serovar D strain NJ1, 79.1 and 81.1% identical to that of the C. psittaci guinea pig inclusion conjunctivitis strain, 60.9 and 62.5% identical to that of the Chlamydia trachomatis L2 strain, and 57.5 and 60.4% identical to that of the Chlamydia pneumoniae IOL-207 strain. The serovar A or D MOMPs were cloned in the mammalian expression plasmid pcDNA1. When pcDNA1/MOMP A or pcDNA1/MOMP D was introduced into COS7 cells, a 40-kDa protein that was identical in size, antigenicity, and electrophoretic mobility to native MOMP was produced. Recombinant MOMP (rMOMP) was located in the cytoplasm of transfected COS7 cells as well as in the plasma membrane and was immunoaccessible. Intramuscular administration of pcDNA1/MOMP in specific-pathogen-free turkeys resulted in local expression of rMOMP in its native conformation, after which anti-MOMP antibodies appeared in the serum.

PCR amplification and sequence of the p33 piroplasm surface antigen gene of a Theileria species isolated from cattle in west Java, Indonesia

Oriental theileriosis, a parasitic disease of cattle caused by protozoa of the Theileria orientalis/sergenti/buffeli group, has been reported in Indonesia but its causal agent had not yet been characterized. This study was carried out to isolate and characterize the parasite through comparison of its p33 piroplasm surface antigen gene sequence, with known p32 sequences of T. sergenti and T. buffeli isolates. A Theileria spp. isolate was collected from an Ongole cow in Jonggol, West-Java, and transferred into a splenectomized calf for antigen production. Piroplasms were extracted from erythrocytes by ammonium chloride-lysis, separated from unlysed leukocytes and parasitic DNA was phenol-extracted. Polymerase chain reaction (PCR) was carried out on genomic DNA with a pair of 20 bp primers showing consensus for the p32-35 nucleotide sequence of 7 known T. orientalis/sergenti/buffeli isolates. An 875 bp fragment was amplified, and further sequenced on both strands by the dye-labeled terminators method. It showed an 88% homology with the p33 nucleotide sequence of the Japanese T. sergenti Ikeda stock and a lesser homology with 6 other sequences of Australian T. buffeli or Japanese T. sergenti stocks. It was shown to share the presence of the Pst 1 and the absence of the HindIII restriction sites of the T. sergenti Ikeda stock and of one Australian T. buffeli stock, respectively. In conclusion, the affiliation to and the relative position of this Indonesian isolate within the T. orientalis/sergenti/buffeli group has been elucidated.

Orthologous DNA sequence variation among 5S ribosomal RNA gene spacer sequences on homoeologous chromosomes 1B, 1D, and 1R of wheat and rye

5S ribosomal gene spacer sequences from the short-spacer arrays of wheat and rye were isolated by PCR. The 29 new DNA sequences displayed noticeable heterogeneity at scattered positions. Nevertheless, based on shared DNA sequence polymorphisms, sequence alignment clearly classified the sequences into three groups. Group-specific primer sets were designed to allow chromosomal assignment by PCR on nullitetrasomic wheat stocks, as well as on wheat-rye translocation and addition lines. The three groups were assigned to orthologous loci 5S-Rrna-B1, 5S-Rrna-D1, and 5S-Rrna-R1 on homoeologous chromosomes 1B, 1D, and 1R, respectively. Hence, group-specific DNA sequence variation could be related to fixed orthologous DNA sequence variation between 5S rRNA multigene families on the homoeologous group 1 chromosomes. In addition, members of the three groups showed fixed orthologous length polymorphism. Four sequenced 5S-Rrna-B1 units, however, had a duplication in the gene encoding region and are probably representatives of a nontranscribed subfamily of 5S rDNA repeating units. The observed chromosome-specific polymorphisms among sequences belonging to a multigene family with thousands of copies suggests that this type of polymorphism may exist in many genes and gene families in polyploid wheats. The implication of this finding in relation to the construction of molecular tools for wheat-genome analysis and manipulation is discussed.Key words: 5S ribosomal RNA loci, nontranscribed spacer, chromosome location, PCR markers, wheat-rye translocation.

Orthologous DNA sequence variation among 5S ribosomal RNA gene spacer sequences on homoeologous chromosomes 1B, 1D, and 1R of wheat and rye

5S ribosomal gene spacer sequences from the short-spacer arrays of wheat and rye were isolated by PCR. The 29 new DNA sequences displayed noticeable heterogeneity at scattered positions. Nevertheless, based on shared DNA sequence polymorphisms, sequence alignment clearly classified the sequences into three groups. Group-specific primer sets were designed to allow chromosomal assignment by PCR on nullitetrasomic wheat stocks, as well as on wheat-rye translocation and addition lines. The three groups were assigned to orthologous loci 5S-Rrna-B1, 5S-Rrna-D1, and 5S-Rrna-R1 on homoeologous chromosomes 1B, 1D, and 1R, respectively. Hence, group-specific DNA sequence variation could be related to fixed orthologous DNA sequence variation between 5S rRNA multigene families on the homoeologous group 1 chromosomes. In addition, members of the three groups showed fixed orthologous length polymorphism. Four sequenced 5S-Rrna-B1 units, however, had a duplication in the gene encoding region and are probably representatives of a nontranscribed subfamily of 5S rDNA repeating units. The observed chromosome-specific polymorphisms among sequences belonging to a multigene family with thousands of copies suggests that this type of polymorphism may exist in many genes and gene families in polyploid wheats. The implication of this finding in relation to the construction of molecular tools for wheat-genome analysis and manipulation is discussed.

Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana

The plant Arabidopsis thaliana (Arabidopsis) has become an important model species for the study of many aspects of plant biology. The relatively small size of the nuclear genome and the availability of extensive physical maps of the five chromosomes provide a feasible basis for initiating sequencing of the five chromosomes. The YAC (yeast artificial chromosome)-based physical map of chromosome 4 was used to construct a sequence-ready map of cosmid and BAC (bacterial artificial chromosome) clones covering a 1.9-megabase (Mb) contiguous region, and the sequence of this region is reported here. Analysis of the sequence revealed an average gene density of one gene every 4.8 kilobases (kb), and 54% of the predicted genes had significant similarity to known genes. Other interesting features were found, such as the sequence of a disease-resistance gene locus, the distribution of retroelements, the frequent occurrence of clustered gene families, and the sequence of several classes of genes not previously encountered in plants.

The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications

In 1992 we started assembling an ordered library of cosmid clones from chromosome XIV of the yeast Saccharomyces cerevisiae. At that time, only 49 genes were known to be located on this chromosome and we estimated that 80% to 90% of its genes were yet to be discovered. In 1993, a team of 20 European laboratories began the systematic sequence analysis of chromosome XIV. The completed and intensively checked final sequence of 784,328 base pairs was released in April, 1996. Substantial parts had been published before or had previously been made available on request. The sequence contained 419 known or presumptive protein-coding genes, including two pseudogenes and three retrotransposons, 14 tRNA genes, and three small nuclear RNA genes. For 116 (30%) protein-coding sequences, one or more structural homologues were identified elsewhere in the yeast genome. Half of them belong to duplicated groups of 6-14 loosely linked genes, in most cases with conserved gene order and orientation (relaxed interchromosomal synteny). We have considered the possible evolutionary origins of this unexpected feature of yeast genome organization.

Sequence analysis of a 37.6 kbp cosmid clone from the right arm of Saccharomyces cerevisiae chromosome XII, carrying YAP3, HOG1, SNR6, tRNA-Arg3 and 23 new open reading frames, among which several homologies to proteins involved in cell division control and to mammalian growth factors and other animal proteins are found

The nucleotide sequence of 37,639 bp of the right arm of chromosome XII has been determined. Twenty-five open reading frames (ORFs) longer than 300 bp were detected, two of which extend into the flanking cosmids. Only two (L2931 and L2961) of the 25 ORFs correspond to previously sequenced genes (HOG1 and YAP3, respectively). Another ORF is distinct from YAP3 but shows pronounced similarity to it. About half of the remaining ORFs show similarity to other genes or display characteristic protein signatures. In particular, ORF L2952 has striking homology with the probable cell cycle control protein crn of Drosophila melanogaster. L2949 has significant similarity to the human ZFM1 (related to a potential suppressor oncogene) and mouse CW17R genes, though it lacks the carboxy-terminal oligoproline and oligoglutamine stretches encoded by these mammalian genes. The small ORF L2922 is similar to part of the much larger yeast flocculation gene FLO1. Other sequences found in the 37639 bp fragment are one delta and one solo-sigma element, the tRNA-Arg3 gene, the small nuclear RNA gene SNR6 and three ARS consensus sequences.

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.