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.

Crystallization and preliminary crystallographic characterization of the extrinsic PsbP protein of photosystem II from Spinacia oleracea.

Preliminary X-ray diffraction analysis of the extrinsic PsbP protein of photosystem II from spinach (Spinacia oleracea) was performed using N-terminally His-tagged recombinant PsbP protein overexpressed in Escherichia coli. Recombinant PsbP protein (thrombin-digested recombinant His-tagged PsbP) stored in bis-Tris buffer pH 6.00 was crystallized using the sitting-drop vapour-diffusion technique with PEG 550 MME as a precipitant and zinc sulfate as an additive. SDS-PAGE analysis of a dissolved crystal showed that the crystals did not contain the degradation products of recombinant PsbP protein. PsbP crystals diffracted to 2.06 A resolution in space group P2(1)2(1)2(1), with unit-cell parameters a = 38.68, b = 46.73, c = 88.9 A.

Phycomyces blakesleeanus TRP1 gene: organization and functional complementation in Escherichia coli and Saccharomyces cerevisiae.

We have cloned the gene encoding the TRPF and TRPC functions of Phycomyces blakesleeanus by complementation of the corresponding activities of Escherichia coli. TRPF also complemented a trpl mutation in Saccharomyces cerevisiae. As in other filamentous fungi, such as Neurospora and Aspergillus spp., the P. blakesleeanus TRPF and TRPC formed part of a trifunctional polypeptide encoded by a single gene (called TRP1). Transcription of TRP1 in P. blakesleeanus did not appear to be regulated by light or by the nutritional status of the culture. The information on the structure and organization of a P. blakesleeanus gene derived from these studies should be useful in devising molecular genetic strategies to analyze the sensory physiology of this organism.

Structural organization of the TRP1 gene of Phycomyces blakesleeanus: implications for evolutionary gene fusion in fungi.

The complete nucleotide (nt) sequence of the cloned TRP1 gene from Phycomyces blakesleeanus is reported. The gene encodes a trifunctional polypeptide that represents a sequential fusion of glutamine amidotransferase (TrpG), indoleglycerolphosphate synthetase (TrpC), and phosphoribosylanthranilate isomerase (TrpF) activities from the amino- to the carboxy terminus. This genetic organization is characteristic of filamentous fungi in general. The transcription start sites and the polyadenylation sites of the gene have been mapped. The two predominant TRP1 transcripts have a short leader of 13 and 18 nt, while minor species with significantly longer leaders are also detectable. Approximately 50 bp and 70 bp upstream from the major transcription start points, sequences that match the canonical eukaryotic TATA and CAAT boxes, respectively, are found. Two major polyadenylation signals are located approximately 50 and 70 nt downstream from the translational stop. Three closely clustered minor polyadenylation sites map to roughly 120-150 bp 3' to the termination codon. The TRP1 gene is the first and only Phycomyces gene that has been cloned and sequenced. The information regarding the promoter and terminator of a Phycomyces gene derived from these studies should benefit strategies aimed at gene manipulations in this organism.

Isocitrate lyase of Ashbya gossypii--transcriptional regulation and peroxisomal localization.

The isocitrate lyase-encoding gene AgICL1 from the filamentous hemiascomycete Ashbya gossypii was isolated by heterologous complementation of a Saccharomyces cerevisiae icl1d mutant. The open reading frame of 1680 bp encoded a protein of 560 amino acids with a calculated molecular weight of 62584. Disruption of the AgICL1 gene led to complete loss of AgIcl1p activity and inability to grow on oleic acid as sole carbon source. Compartmentation of AgIcl1p in peroxisomes was demonstrated both by Percoll density gradient centrifugation and by immunogold labeling of ultrathin sections using specific antibodies. This fitted with the peroxisomal targeting signal AKL predicted from the C-terminal DNA sequence. Northern blot analysis with mycelium grown on different carbon sources as well as AgICL1 promoter replacement with the constitutive AgTEF promoter revealed a regulation at the transcriptional level. AgICL1 was subject to glucose repression, derepressed by glycerol, partially induced by the C2 compounds ethanol and acetate, and fully induced by soybean oil.

Photoregulation of carotenogenesis in Phycomyces.

Mutants of Phycomyces defective in carotene regulation were studied in relation with the photo carotenogenic response. Quantitative complementation analyses revealed that carC, carA and carS mutations are recessive and complement for this photoresponse in carC * carA and carC * carS heterokaryons. A scheme of the regulation of carotenogenesis by light is proposed.

Transformation of Phycomyces blakesleeanus to G-418 resistance by an autonomously replicating plasmid.

The fungus, Phycomyces blakesleeanus, shows many well-defined responses to a number of external stimuli. Genetic analysis shows that at least eight genes are involved in Phycomyces sensory transduction. As a first step toward the molecular analysis of these genes and their products, we have developed a transformation protocol for Phycomyces by using a plasmid containing the kanamycin-resistance gene from Tn903 and a Phycomyces DNA fragment capable of supporting autonomous replication in yeast (ARS). Our results demonstrate that the Tn903 gene is expressed in Phycomyces and that the ARS fragment selected in yeast supports autonomous replication in Phycomyces as well.

Three biotechnical processes using Ashbya gossypii, Candida famata, or Bacillus subtilis compete with chemical riboflavin production.

Chemical riboflavin production, successfully used for decades, is in the course of being replaced by microbial processes. These promise to save half the costs, reduce waste and energy requirements, and use renewable resources like sugar or plant oil. Three microorganisms are currently in use for industrial riboflavin production. The hemiascomycetes Ashbya gossypii, a filamentous fungus, and Candida famata, a yeast, are naturally occurring overproducers of this vitamin. To obtain riboflavin production with the gram-positive bacterium Bacillus subtilis requires at least the deregulation of purine synthesis and a mutation in a flavokinase/FAD-synthetase. It is common to all three organisms that riboflavin production is recognizable by the yellow color of the colonies. This is an important tool for the screening of improved mutants. Antimetabolites like itaconate, which inhibits the isocitrate lyase in A. gossypii, tubercidin, which inhibits purine biosynthesis in C. famata, or roseoflavin, a structural analog of riboflavin used for B. subtilis, have been applied successfully for mutant selections. The production of riboflavin by the two fungi seems to be limited by precursor supply, as was concluded from feeding and gene-overexpression experiments. Although flux studies in B. subtilis revealed an increase both in maintenance metabolism and in the oxidative part of the pentose phosphate pathway, the major limitation there seems to be the riboflavin pathway. Multiple copies of the rib genes and promoter replacements are necessary to achieve competitive productivity.

Carrier-mediated transport of riboflavin in Ashbya gossypii.

The filamentous hemiascomycete Ashbya gossypii is used for industrial riboflavin production. We examined riboflavin uptake and excretion at the plasma membrane using riboflavin auxotrophic and overproducing mutants. The riboflavin uptake system had low activity [Vmax = 20 +/- 4 nmol min(-1) g(-1) mycelial dry weight (dw)] and high affinity (KM = 40 +/- 12 microM). Inhibitor studies with the analogs FMN and FAD revealed high specificity of the uptake system. Excretion of riboflavin was not the consequence of non-specific permeability of the plasma membrane. Excretion rates in the mid-production phase were determined to be 2.5 nmol min(-1) g(-1) dw for wild-type cells and 66.7 nmol min(-1) g(-1) dw for an overproducing mutant, respectively. Inhibition of the reverse reaction, riboflavin uptake, led to an increase in apparent riboflavin efflux in the early production phase, indicating the presence of a separate excretion carrier. Riboflavin accumulation in A. gossypii vacuoles leading to product retention was found to be a secondary transport process. To address the question of whether a flux from the vacuoles back into the cytoplasm is present, we characterized efflux in hyphae in which the plasma membrane was permeabilized with digitonin. Efflux kinetics across the vacuolar membrane were unaffected by the lack of vacuolar H+ATPase activity and ATP, suggesting a passive mechanism. Based on the characterization of riboflavin transport processes in this study, the design of new production strains with improved riboflavin excretion may be possible.

Molecular characterization of FMN1, the structural gene for the monofunctional flavokinase of Saccharomyces cerevisiae.

Flavokinase catalyzes the transfer of the gamma-phosphoryl group of ATP to riboflavin to form the flavocoenzyme FMN. Consistent patterns of sequence similarities have identified the open reading frame of unknown function YDR236c as a candidate to encode flavokinase in Saccharomyces cerevisiae. In order to determine whether the product of this gene corresponds to yeast flavokinase, its coding region was amplified from S. cerevisiae genomic DNA by polymerase chain reaction and expressed in Escherichia coli. The purified form of the expressed recombinant protein efficiently catalyzed the formation of FMN from riboflavin and ATP. In contrast to bifunctional prokaryotic flavokinase/FAD synthetase enzymes, the yeast enzyme did not show accompanying FAD synthetase activity. Deletion of YDR236c produced yeast mutants unable to grow on rich medium; however, the growth of the ydr236cDelta mutants could be rescued by the addition of FMN to the medium. Overexpression of YDR236c caused a 50-fold increase in flavokinase specific activity in yeast cells. These findings demonstrate that YDR236c corresponds to the gene encoding a monofunctional flavokinase in yeast, which we propose to be designated as FMN1. The FMN1 gene codes for a 25-kDa protein with characteristics of signals for import into mitochondria. By immunoblotting analysis of Saccharomyces subcellular fractions, we provide evidence that the Fmn1 protein is localized in microsomes and in mitochondria. Analysis of submitochondrial fractions revealed that the mitochondrial form of Fmn1p is an integral protein of the inner membrane exposing its COOH-terminal domain to the matrix space. A similarity search in the data base banks revealed the presence of sequences homologous to yeast flavokinase in the genome of several eukaryotic organisms such as Schizosaccharomyces pombe, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, and humans.

[Integrated treatment of psychosis: combination of psychopharmacology and psychotherapy]. / El tratamiento integrado de la psicosis: combinación de psicofármacos y psicoterapia.

Over the initial period of its clinical use, the effectiveness of neuroleptics determined a relative decline of the psychotherapeutic approaches to the psychoses. However, recent evidence shows that combined pharmacological-psychotherapeutic treatment may increase therapeutic potency. The specific psychodynamics of psychotic syndromes requires the association of different psychotherapeutic techniques and patient management approaches to pharmacological treatment.

[Stress and anxiety]. / Estrés y ansiedad.

Stressful events, either of traumatic quality or of lesser intensity but repetitive, are a frequent antecedent in the development of anxiety disorders. The Stress Reactivity Index modulates the intensity of the "life event effect", and can be considered as a marker of vulnerability to stress. In susceptible subjects, a vicious circle process tends to feed the anxiety-producing mechanisms, long after the original initiating factors have disappeared.

The Saccharomyces cerevisiae RIB4 gene codes for 6,7-dimethyl-8-ribityllumazine synthase involved in riboflavin biosynthesis. Molecular characterization of the gene and purification of the encoded protein.

6,7-Dimethyl-8-ribityllumazine, the immediate biosynthetic precursor of riboflavin, is synthesized by condensation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy-2-butanone 4-phosphate. The gene coding for 6,7-dimethyl-8-ribityllumazine synthase in Saccharomyces cerevisiae (RIB4) has been cloned by functional complementation of a mutant accumulating 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, which can grow on riboflavin- or diacetyl- but not on 3,4-dihydroxy-2-butanone-supplemented media. Gene disruption of the chromosomal copy of RIB4 led to riboflavin auxotrophy and loss of enzyme activity. Nucleotide sequencing revealed a 169-base pair open reading frame encoding a 18.6-kDa protein. Hybridization analysis indicated that RIB4 is a single copy gene located on the left arm of chromosome XV. Overexpression of the RIB4 coding sequence in yeast cells under the control of the strong TEF1 promoter allowed ready purification of 6,7-dimethyl-8-ribityllumazine synthase to apparent homogeneity by a simple procedure. Initial structural characterization of 6,7-dimethyl-8-ribityllumazine synthase by gel filtration chromatography and both nondenaturing pore limit and SDS-polyacrylamide gel electrophoresis showed that the enzyme forms a pentamer of identical 16.8-kDa subunits. The derived amino acid sequence of RIB4 shows extensive homology to the sequences of the beta subunits of riboflavin synthase from Bacillus subtilis and other prokaryotes.

[Stress reactivity and affective psychopathology in health care workers]. / Reactividad al estrés y patología afectiva en personal sanitario.

While the etiology of the affective disorders remain unknown, most believe that interactions between genetic and environmental factors are critical. Stress has been implicated as an important factor related to the onset and progression of affective disorders. Characteristics rendering individuals more or less vulnerable to stress are very important to elucidate and will be relevant to understanding the pathophysiology of affective disorders. Stress reactivity could be one of these individual characteristics since the results of the present paper show a statistically significant correlation between stress reactivity and the affective psychopathology observed.

The sequence of a 20.3 kb DNA fragment from the left arm of Saccharomyces cerevisiae chromosome IV contains the KIN28, MSS2, PHO2, POL3 and DUN1 genes, and six new open reading frames.

We report the sequence of a 20 300 bp DNA fragment from the left arm of Saccharomyces cerevisiae chromosome IV. This segment contains 13 complete open reading frames (ORFs) and part of another ORF, altogether covering 84.2% of the entire sequence, five of which correspond to the previously characterized KIN28, MSS2, PHO2, POL3/CDC2 and DUN1 genes. One putative protein, D2358p, shares considerable homology with an O-sialoglycoprotein endopeptidase from Pasteurella haemolytica serotype A1. The putative product of D2325 contains the characteristic consensus motif of triacylglycerol lipases. D2320p and D2352p have a putative 'leucine-zipper' structure and a RNA-binding region Rnp-1 signature, respectively.

Riboflavin biosynthesis in Saccharomyces cerevisiae. Cloning, characterization, and expression of the RIB5 gene encoding riboflavin synthase.

Saccharomyces cerevisiae has a monofunctional riboflavin synthase that catalyzes the formation of riboflavin from 6,7-dimethyl-8-ribityllumazine. We have isolated the gene encoding this enzyme from a yeast genomic library by functional complementation of a mutant, rib5-10, lacking riboflavin synthase activity. Deletion of the chromosomal copy of RIB5 led to riboflavin auxotrophy and loss of enzyme activity. Intragenic complementation between point and deletion mutant alleles suggested that the encoded protein (Rib5p) assembles into a multimeric complex and predicted the existence of a discrete functional domain located at the N terminus. Nucleotide sequencing revealed a 714-base pair open reading frame encoding a 25-kDa protein. Rib5p was purified to apparent homogeneity by a simple procedure. The specific activity of the enzyme was enriched 8500-fold. The N-terminal sequence of the purified enzyme was identical to the sequence predicted from the nucleotide sequence of the RIB5 gene. Initial structural characterization of riboflavin synthase by gel filtration chromatography and both nondenaturing pore limit and SDS-polyacrylamide gel electrophoresis showed that the enzyme forms a trimer of identical 25-kDa subunits. The derived amino acid sequence of RIB5 shows extensive homology to the sequences of the alpha subunits of riboflavin synthase from Bacillus subtilis and other prokaryotes. In addition, the sequence also shows internal homology between the N-terminal and the C-terminal halves of the protein. Taken together, these results suggest that the Rib5p subunit contains two structurally related (substrate-binding) but catalytically different (acceptor and donator) domains.

Disruption and basic phenotypic analysis of six novel genes from the left arm of chromosome XIV of Saccharomyces cerevisiae.

We describe here the construction of six deletion mutants and their basic phenotypic analysis in three different backgrounds. The six genes were disrupted in three diploid strains (FY1679, W303 and CEN.PK2) by the long flanking homology (LFH) method (Wach, 1996). Transformants were selected as geneticin (G418)-resistant colonies and correct integration of the kanMX4 cassette was checked by colony PCR. Following sporulation of the heterozygous diploids, tetrads were dissected and scored for segregation of G418-resistance and auxotrophic markers. One of the six ORFs (YNL158w) corresponds to an essential gene which has no homology with other genes present in the databases and has two predicted transmembrane domains. Growth tests performed on different media at 15 degrees C, 30 degrees C or 37 degrees C with haploid deletants of the five non-essential genes revealed no apparent phenotype in any of them.

Disruption of six unknown open reading frames from Saccharomyces cerevisiae reveals two genes involved in vacuolar morphogenesis and one gene required for sporulation.

In this report we describe the construction and basic phenotypic analysis of deletion mutants in six open reading frames (ORFs) of unknown function from the yeast Saccharomyces cerevisiae. Using the dominant kanMX marker and polymerase chain reaction (PCR) methods, deletion cassettes were constructed for five ORFs (YNL099c, YNL100w, YNL101w, YNL106c and YNL242w) located on chromosome XIV and one ORF (YOR109w) located on chromosome XV. The recovery of viable haploid deletant strains among the meiotic products of heterozygous deletants for each ORF demonstrated that none of the analysed ORFs was essential. With the exception of YNL242w, no alterations in growth characteristics or mating and sporulation efficiencies associated with deletion of the ORFs were observed. Homozygous diploid ynl242w delta cells obtained in three different genetic backgrounds were unable to sporulate, indicating that the product of this ORF is required for sporulation. Complementation of the sporulation defect by the cognate gene clone confirmed this observation. YNL106c and YOR109w are very similar and show strong sequence homology with a mammalian phosphatidylinositol-phosphate 5-phosphatase, synaptojanin, known to be involved in synaptic vesicle cycling. Strains bearing single and double deletions of YNL106c and YOR109w were seen to display abnormal vacuolar morphologies of varying degrees. Complementation tests indicated that YNL106c and YOR109w are redundant genes.

Physiological consequence of disruption of the VMA1 gene in the riboflavin overproducer Ashbya gossypii.

The vacuolar ATPase subunit A structural gene VMA1 of the biotechnologically important riboflavin overproducer Ashbya gossypii was cloned and disrupted to prevent riboflavin retention in the vacuolar compartment and to redirect the riboflavin flux into the medium. Cloning was achieved by polymerase chain reaction using oligonucleotide primers derived form conserved sequences of the Vma1 proteins from yeast and filamentous fungi. The deduced polypeptide comprises 617 amino acids with a calculated molecular mass of 67.8 kDa. The deduced amino acid sequence is highly similar to that of the catalytic subunits of Saccharomyces cerevisiae (67 kDa), Candida tropicalis (67 kDa), and Neurospora crassa (67 kDa) with 89, 87, and 60% identity, respectively, and shows about 25% identity to the beta-subunit of the FoF1-ATPase of S. cerevisiae and Schizosaccharomyces pombe. In contrast to S. cerevisiae, however, where disruption of the VMA1 gene was conditionally lethal, and to N. crassa, where viable disruptants could not be isolated, disruption of the VMA1 gene in A. gossypii did not cause a lethal phenotype. Disruption of the AgVMA1 gene led to complete excretion of riboflavin into the medium instead of retention in the vacuolar compartment, as observed in the wild type.

DNA sequencing and analysis of a 40 kb region from the right arm of chromosome II from Schizosaccharomyces pombe.

We have determined the complete nucleotide sequence of a 39,648 bp segment, contained in cosmid c32F12, derived from the right arm of chromosome II from the fission yeast Schizosaccharomyces pombe. Computer analysis of the sequence revealed the presence of 15 non-overlapping open reading-frames (ORFs) longer than 300 bp and one tRNA-Thr gene. Six ORFs correspond to the previously known rec14+, tug1+, rum1+, pch1+, gpd1+ and cyr1+ genes. Five ORFs code for putative proteins with significant homology to proteins from other organisms. SPBC32F12.01c shows considerable similarity to human neutral sphingomyelinase, whereas SPBC32F12.03c, SPBC32F12.10 and SPBC32F12.14 exhibit strong homology to glutathione peroxidase, phosphoglucomutase and ubiquitin protein ligase E-3 components from various organisms, respectively. The four remaining ORFs identified show weak or non-significant homology to previously sequenced genes. The nucleotide sequence has been submitted to the EMBL database under Accession Number AL023796.