Two mutually exclusive regulatory systems inhibit UASGATA, a cluster of 5'-GAT(A/T)A-3' upstream from the UGA4 gene of Saccharomyces cerevisiae

The S. cerevisiae Uga43(Dal80) protein down-regulates the expression of multiple nitrogen pathway genes. It contains a zinc-finger motif similar to the DNA-binding domain of the vertebrate GATA family of transcription factors; this domain is known to direct binding to 5'-GATA-3' core sequences. The inducible UGA4 gene, which encodes the specific gamma-aminobutyrate permease, undergoes strong repression by Uga43p. This study shows that the 5' region of UGA4 contains a UAS element made of four directly repeated 5'-CGAT(A/T) AG-3' sequences. This element, called UASGATA, can potentially confer to the UGA4 gene high-level expression in the absence of inducer, but this potential activity is inhibited by two distinct repression systems. One system is Uga43p-dependent; it operates in cells grown on a poor nitrogen source. The other is the nitrogen repression system, which relies on Ure2p and glutamine and operates when a good nitrogen source is present. Nitrogen repression also blocks the synthesis of Uga43p, making the two repression systems mutually exclusive. Previous studies have shown that expression supported by 5'-GATA-3'-containing UAS elements requires Gln3p, another global nitrogen regulatory factor containing a GATA zinc-finger domain. Although Gln3p contributes to UASGATA activity, evidence suggests that a second factor can potentially direct expression through UASGATA. Expression conferred by this putative factor is subject to both Uga43p- and Ure2p-mediated repression. The role of UASGATA in the expression of the UGA4 gene is discussed in relation to its sensitivity to the two distinct repression systems.

WWP, a new amino acid motif present in single or multiple copies in various proteins including dystrophin and the SH3-binding Yes-associated protein YAP65

A new repeating amino acid motif, which we called WWP, was found in several proteins of yeast, nematod or vertebrate origin. Among these are dystrophin, the product of the Duchenne muscular dystrophy locus, a protein (YAP65) which associates in vitro with the Src homology domain 3 (SH3) of the Yes proto-oncogene product, and a human putative GTPase-activating protein. As is the case for proteins which contain the SH2, SH3 and PH domains, at least some of the WWP-containing proteins appear to be signaling or cytoskeletal proteins, associated with plasma or organellar membranes, and specific protein-protein contacts are likely to be crucial to their function.

Complete DNA sequence of yeast chromosome II

In the framework of the EU genome-sequencing programmes, the complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome II (807 188 bp) has been determined. At present, this is the largest eukaryotic chromosome entirely sequenced. A total of 410 open reading frames (ORFs) were identified, covering 72% of the sequence. Similarity searches revealed that 124 ORFs (30%) correspond to genes of known function, 51 ORFs (12.5%) appear to be homologues of genes whose functions are known, 52 others (12.5%) have homologues the functions of which are not well defined and another 33 of the novel putative genes (8%) exhibit a degree of similarity which is insufficient to confidently assign function. Of the genes on chromosome II, 37-45% are thus of unpredicted function. Among the novel putative genes, we found several that are related to genes that perform differentiated functions in multicellular organisms of are involved in malignancy. In addition to a compact arrangement of potential protein coding sequences, the analysis of this chromosome confirmed general chromosome patterns but also revealed particular novel features of chromosomal organization. Alternating regional variations in average base composition correlate with variations in local gene density along chromosome II, as observed in chromosomes XI and III. We propose that functional ARS elements are preferably located in the AT-rich regions that have a spacing of approximately 110 kb. Similarly, the 13 tRNA genes and the three Ty elements of chromosome II are found in AT-rich regions. In chromosome II, the distribution of coding sequences between the two strands is biased, with a ratio of 1.3:1. An interesting aspect regarding the evolution of the eukaryotic genome is the finding that chromosome II has a high degree of internal genetic redundancy, amounting to 16% of the coding capacity.

Optimized vertical stereo base radiographic setup for the clinical three-dimensional reconstruction of the human spine

This paper presents a method to determine the stereoradiographic planes and anatomical vertebral landmarks giving the most reliable three-dimensional reconstructions of the thoracic and lumbar spine for clinical studies. The present investigation was limited to stereoradiographic setups with a normal vertical stereo base. Possible X-ray tube positions are thus corresponding to angles ranging from 0 (conventional posteroanterior radiograph) up to 30 degrees (dimension of the X-ray room). An X-ray phantom was used as a specimen from which three-dimensional reconstructions with the direct linear transformation (DLT) algorithm were obtained. Visibility of landmarks located on pedicles, end-plates, transverse and spinous processes was evaluated for the whole thoracic and lumbar spine (T1 to L5). Process landmarks were discarded because their poor visibility on radiographs produced inaccurate three-dimensional reconstructions. Considering the size, shape and orientation of vertebrae, an angle of 20 degrees between the posteroanterior horizontal position and the angled position of the X-ray tube gave optimal results. Landmarks located on pedicles and end-plates produced the most reliable three-dimensional reconstructions of the spine. Pedicles were found to be more reliable landmarks than end-plates. Validation of the technique with reconstructed steel beads reveals three-dimensional errors under 1.0 mm. Since vertebral landmarks were more difficult to identify on radiographs than steel beads, reconstruction results were compared with those obtained with a biplanar orthogonal setup. This shows that three-dimensional errors of 8.0 mm may be expected on actual reconstructions of the spine and errors as large as 15.0 mm may be present on poorly visible landmarks.

Cloning and expression of the MEP1 gene encoding an ammonium transporter in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, the transport of ammonium across the plasma membrane for use as a nitrogen source is mediated by at least two functionally distinct transport systems whose respective encoding genes are called MEP1 and MEP2. Mutations in the MEP2 gene affect high affinity, low capacity ammonium transport while mutations in the MEP1 gene disrupt a lower affinity, higher capacity system. In this work, the MEP1 gene has been cloned and sequenced and its expression analyzed. The predicted amino acid sequence reveals a highly hydrophobic, 54 kDa protein with 10 or 11 putative membrane-spanning regions. The predicted Mep1p protein shares high sequence similarity with several bacterial proteins of unknown function, notably the product of the nitrogen-regulated nrgA gene of Bacillus subtilis, and with that of a partial cDNA sequence derived from Caenorhabditis elegans. The Mep1p and related proteins appear to define a new family of transmembrane proteins evolutionarily conserved in at least bacteria, fungi and animals. The MEP1 gene is most highly expressed when the cells are grown on low concentrations of ammonium or on 'poor' nitrogen sources like urea or proline. It is down-regulated, on the other hand, when the concentration of ammonium is high or when other 'good' nitrogen sources like glutamine or asparagine are supplied in the culture medium. The overall properties of Mep1p indicate that it is a transporter of ammonium. Its main function appears to be to enable cells grown under nitrogen-limiting conditions to incorporate ammonium present at relatively low concentrations in the growth medium.

Complete DNA sequence of yeast chromosome XI

The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome XI has been determined. In addition to a compact arrangement of potential protein coding sequences, the 666,448-base-pair sequence has revealed general chromosome patterns; in particular, alternating regional variations in average base composition correlate with variations in local gene density along the chromosome. Significant discrepancies with the previously published genetic map demonstrate the need for using independent physical mapping criteria.

[Oncologic application of oocyte donation]

Antimitotic chemotherapy and/or radiation therapy can induce a premature ovarian failure in women. The improvement of the prognosis of cancer and the increasing in long-term survival mean that preservation of fertility should be considered before initiating therapy. An embryo cryopreservation can be proposed if the circumstances allow that possibility. Ten young women were included in our program and benefited from an oocyte retrieval before cancer therapy. Nine of them had an embryo cryopreservation, and one without partner an oocyte cryopreservation. Three patients had an embryo replacement without success, and in one case, a spontaneous full-term pregnancy was obtained after ovarian detransposition through coelioscopy. In the future, oocyte cryopreservation could appear a more suitable answer. Actually, oocyte donation with estrogen and progesterone replacement therapy gives good results (in our experience, 23.2 per cent of ongoing pregnancies per transfer). Nevertheless, after treatment against cancer, a study of the uterus with its arteries, and a particular adaptation of the treatment are necessary because of the risks of tissue damage impairing the embryo implantation. Indeed, in fifteen patients included in this group, eight women had fourteen transfers unfortunately without success. Consequently, the seven other women underwent complementary examinations. Two embryos were replaced in one patient with a more adjustable treatment allowing a full-term pregnancy.

The increased risk of complication observed in singleton pregnancies resulting from in-vitro fertilization (IVF) does not seem to be related to the IVF method itself

Singleton pregnancies resulting from in-vitro fertilization (IVF) seem to have an increased risk of obstetric and paediatric complications. In a retrospective study we compared, during the same period, 162 IVF singleton pregnancies with 263 pregnancies resulting from stimulated cycles (without IVF) and with 5096 natural pregnancies. No significant difference was found between the first two groups concerning complications (i.e. prematurity, low birthweight, small-for-gestational-age and perinatal mortality). The results indicate that an adverse outcome is more common for pregnancies after ovarian stimulation (with or without IVF) compared to natural pregnancies. Therefore the increased risk does not appear to be linked to the IVF method itself but rather to a common factor in these two populations, i.e. population characteristics, underlying infertile status and/or ovarian stimulation.

Cloning and expression of the UGA4 gene coding for the inducible GABA-specific transport protein of Saccharomyces cerevisiae

Transport of 4-aminobutyric acid (GABA) in Saccharomyces cerevisiae is mediated by three transport systems: the general amino acid permease (GAP1 gene), the proline permease (PUT4 gene), and a specific GABA permease (UGA4 gene) which is induced in the presence of GABA. The UGA4 gene encoding the inducible GABA-specific transporter was cloned and sequenced and its expression analyzed. The predicted amino acid sequence shows that UGA4 encodes a 62 kDa protein having 9-12 putative membrane-spanning regions. The predicted UGA4 protein shares significant sequence similarity with the yeast choline transporter (CTR gene), exhibiting but limited similarity to the previously reported GABA transporters, i.e. the yeast GAP1 and PUT4 permeases and the rat brain GAT-1 transporter. Induction of UGA4 in the presence of GABA is exerted at the level of UGA4 mRNA accumulation, most probably at the level of transcription itself. This induction is conferred by the 5' flanking region and requires the integrity of two positive regulatory proteins, the inducer-specific factor UGA3 and the pleiotropic factor UGA35/DURL/DAL81. In the absence of the pleiotropic UGA43/DAL80 repressor, UGA4 is constitutively expressed at high level.

Effect of radiographic landmark identification errors on the accuracy of three-dimensional reconstruction of the human spine

In three-dimensional reconstruction of the human spine obtained from stereo-radiographic set-ups (two radiographs or more), it is extremely difficult to identify exactly the same landmarks on all radiographs. The effect of these identification errors was investigated with simulations made on points of known three-dimensional co-ordinates and compared with three-dimensional reconstructions of real spines obtained with the direct linear transformation algorithm. Results showed that radiographic identification errors of up to 2 mm were common, causing reconstruction errors of up to 5 mm. These reconstruction errors may be noticed in the form of geometrical inaccuracies in the graphical representation of three-dimensional reconstructions of the spine. Successive displacements were then imposed on image point co-ordinates to minimise the identification error and increase the reconstruction accuracy. The improvement on the three-dimensional reconstruction results was negligible. Three-dimensional reconstructions obtained from three radiographs were also investigated. They showed slightly more accurate reconstructions than those obtained from two radiographs. However, the increase of X-ray exposure on the patient may not be worthwhile.

The UGA43 negative regulatory gene of Saccharomyces cerevisiae contains both a GATA-1 type zinc finger and a putative leucine zipper

The UGA43 gene of Saccharomyces cerevisiae is required for repression of inducible genes involved in the utilization of 4-aminobutyric acid (GABA) or urea as nitrogen sources. The UGA43 gene has been cloned by complementation of a uga43 mutation. The N-terminal region of the UGA43 protein is very similar to the DNA-binding zinc-finger region typical of the GATA regulatory factor family in vertebrates. UGA43 is the first reported instance of a GATA protein with a negative regulatory function. The C-terminal region of the predicted UGA43 protein contains a putative leucine zipper. Sequencing of three uga43 mutant alleles suggests that the GATA and putative leucine-zipper regions are both required for the repressive activity of UGA43. UGA43 appears to be a highly regulated gene. On "poor" nitrogen sources, UGA43 transcripts are measured at high levels whereas they are nearly undetectable in conditions of nitrogen catabolite repression. The levels measured on "poor" nitrogen sources are further increased in uga43 mutant cells, suggesting that UGA43 exerts negative autoregulation.

Stimulation by auxin of phospholipase A in membrane vesicles from an auxin-sensitive tissue is mediated by an auxin receptor

Microsomal vesicles were prepared from zucchini (Cucurbita pepo L.) hypocotyls containing radioactive phosphatidylethanolamine or phosphatidylcholine, and these lipids were used as substrates by phospholipase A which is activated by auxins. Phospholipase D and phospholipase C hydrolysed the same substrates but were not influenced by auxin. Phospholipase A was activated by the auxins indolyl-3-acetic acid, 2,4-dichlorophenoxyacetic acid and, to a lesser extent, by α-naphthaleneacetic acid whereas the weak auxins 2,3-dichlorophenoxyacetic acid and β-naphthaleneacetic acid were almost inactive. This hormone specificity was also found in growth tests with etiolated zucchini hypocotyls. Phospholipase A activation by auxin was blocked by a polyclonal antibody against the maize auxin-binding protein. We propose that phospholipase A activation is a primary reaction in the signal transduction leading from hormone-binding to the growth response.

Modulation of proteolytic activity during neuritogenesis in the PC12 nerve cell: differential control of plasminogen activator and plasminogen activator inhibitor activities by nerve growth factor and dibutyryl-cyclic AMP

Extracellular proteolysis is considered to be required during neuritic outgrowth to control the adhesiveness between the growing neurite membrane and extracellular matrix proteins. In this work, PC12 nerve cells were used to study the modulation of proteolytic activity during neuronal differentiation. PC12 cells were found to contain and release a 70-75-kDa tissue-type plasminogen activator (tPA) and a much less abundant 48-kDa urokinase-type plasminogen activator. A plasminogen activator inhibitor (PAI) activity with molecular sizes of 54 and 58 kDa was also detected in PC12 cell conditioned medium and formed high-molecular-mass complexes with released tPA. Release of PAI activity was dependent on treatment with nerve growth factor (NGF), whereas tPA synthesis and release were under control of a cyclic AMP-dependent mechanism and increased on treatment with dibutyryl-cyclic AMP [(But)2cAMP] or cholera toxin. Simultaneous treatment with NGF and (But)2cAMP resulted in increases of both tPA and PAI release and enhancement of tPA-PAI complex formation. The resulting plasminogen activator activity in conditioned medium was high in (But)2cAMP-treated cultures with short neuritic outgrowth but remained low in NGF- or NGF plus (But)2cAMP-treated cultures, where neurite extension was, respectively, large and very large. These results suggest that excess proteolytic activity may be detrimental to neuritic outgrowth and that not only PAI release but also tPA-PAI complex formation is associated with production of large and stable neuritic outgrowth. This can be understood as an involvement of PAI in the protection against neurite-destabilizing proteolytic activity.

The UGA3 gene regulating the GABA catabolic pathway in Saccharomyces cerevisiae codes for a putative zinc-finger protein acting on RNA amount

The UGA3 gene of Saccharomyces cerevisiae is required for 4-aminobutyric acid (GABA)-dependent induction of the UGA1, UGA2 and UGA4 genes which encode the two GABA catabolic enzymes and a GABA-specific permease, respectively. Measurements of UGA1-specific transcripts show that induction of UGA1 correlates with accumulation of its RNA and requires a functional UGA3 gene. A 2 kb DNA fragment complementing the uga3 mutation was isolated and shown to contain the UGA3 gene. The primary structure of the UGA3 encoded protein was deduced from the DNA sequence, and contains an N-terminal, cysteine-rich motif similar in sequence to regions found in other fungal regulatory proteins and which are supposed to form zinc finger structures involved in DNA binding. Mutations were identified in the UGA3 genes isolated from uninducible and constitutive uga3 alleles. One case of intragenic complementation between two uninducible uga3 mutants is reported, indicating a possible oligomeric structure for UGAe. The role of UGA3 is discussed in relation to its genetic properties and its predicted structure.

A rapid response to a plant hormone: auxin stimulates phospholipase A2 in vivo and in vitro

Addition of the active auxins indole-3-acetic acid, 2,4-dichlorophenoxyacetic acid or alpha-naphthylacetic acid to cultured soybean (Glycine max L.) cells prelabeled with ethanolamine or choline increased the radioactivity in the lysophosphatidylethanolamine (LPE) or lysophosphatidylcholine (LPC) pool within 5 min. The inactive auxin analogue, beta-naphthylacetic acid, was inactive in this response. In membranes prelabeled in vivo, either with ethanolamine or choline, and subsequently isolated from zucchini (Cucurbita pepo L.) hypocotyls, indole-3-acetic acid and 2,4-dichlorophenoxyacetic acid stimulated the conversion of phosphatidylethanolamine (PE) to LPE and of phosphatidylcholine (PC) to LPC in vitro whereas the inactive auxin analogue 2,3-dichlorophenoxyacetic acid did not.

Mutant and chimeric recombinant plasminogen activators. Production in eukaryotic cells and preliminary characterization

Mutant urokinase-type plasminogen activator (u-PA) genes and hybrid genes between tissue-type plasminogen activator (t-PA) and u-PA have been designed to direct the synthesis of new plasminogen activators and to investigate the structure-function relationship in these molecules. The following classes of constructs were made starting from cDNA encoding human t-PA or u-PA: 1) u-PA mutants in which the Arg156 and Lys158 were substituted with threonine, thus preventing cleavage by thrombin and plasmin; 2) hybrid molecules in which the NH2-terminal regions of t-PA (amino acid residues 1-67, 1-262, or 1-313) were fused with the COOH-terminal region of u-PA (amino acids 136-411, 139-411, or 195-411, respectively); and 3) a hybrid molecule in which the second kringle of t-PA (amino acids 173-262) was inserted between amino acids 130 and 139 of u-PA. In all cases but one, the recombinant proteins, produced by transfected eukaryotic cells, were efficiently secreted in the culture medium. The translation products have been tested for their ability to activate plasminogen after in situ binding to an insolubilized monoclonal antibody directed against urokinase. All recombinant enzymes were shown to be active, except those in which Lys158 of u-PA was substituted with threonine. Recombination of structural regions derived from t-PA, such as the finger, the kringle 2, or most of the A-chain sequences, with the protease part or the complete u-PA molecule did not impair the catalytic activity of the hybrid polypeptides. This observation supports the hypothesis that structural domains in t-PA and u-PA fold independently from one to another.