A 6940 bp DNA fragment from Desulfovibrio gigas contains genes coding for lipoproteins, universal stress response and transcriptional regulator protein homologues

The nucleotide sequence of a 6940 bp DNA fragment from Desulfovibrio gigas, containing seven ORFs was determined. ORF-1 encodes a probable lipoprotein having high similarities with lytic transglycosylases. ORF-2 encodes a polypeptide that does not show homologies with proteins deposited in the database, but it contains the consensus pattern of class II aminoacyl-tRNA synthetases. The putative protein encoded by ORF-3 possesses high similarities with universal stress response proteins from the UspA family. Northern blot analysis of ORF-3 shows that it is constitutively and abundantly expressed. ORF-4 encodes a probable helix-turn-helix-containing DNA-binding protein, given the presence of the helix-turn-helix motif, characteristic of this class of proteins. Its N-terminal region has high identity with its counterparts from proteins belonging to the RRF2 family. Northern blot analysis shows that ORF-4 is transcribed as a single mRNA in contrast to its orthologue from Desulfovibrio vulgaris. ORF-5 encodes a putative fusion protein as its N- and C-termini show significant homologies with molybdenum formylmethanofuran dehydrogenase and molybdopterin biosynthesis proteins, respectively. ORF-7 encodes a prokaryotic lipoprotein having homologies with multidrug efflux and DNA damage-inducible proteins, and it is constitutively and abundantly expressed.

Molecular characterization of Desulfovibrio gigas neelaredoxin, a protein involved in oxygen detoxification in anaerobes

Desulfovibrio gigas neelaredoxin is an iron-containing protein of 15 kDa, having a single iron site with a His(4)Cys coordination. Neelaredoxins and homologous proteins are widespread in anaerobic prokaryotes and have superoxide-scavenging activity. To further understand its role in anaerobes, its genomic organization and expression in D. gigas were studied and its ability to complement Escherichia coli superoxide dismutase deletion mutant was assessed. In D. gigas, neelaredoxin is transcribed as a monocistronic mRNA of 500 bases as revealed by Northern analysis. Putative promoter elements resembling sigma(70) recognition sequences were identified. Neelaredoxin is abundantly and constitutively expressed, and its expression is not further induced during treatment with O(2) or H(2)O(2). The neelaredoxin gene was cloned by PCR and expressed in E. coli, and the protein was purified to homogeneity. The recombinant neelaredoxin has spectroscopic properties identical to those observed for the native one. Mutations of Cys-115, one of the iron ligands, show that this ligand is essential for the activity of neelaredoxin. In an attempt to elucidate the function of neelaredoxin within the cell, it was expressed in an E. coli mutant deficient in cytoplasmic superoxide dismutases (sodA sodB). Neelaredoxin suppresses the deleterious effects produced by superoxide, indicating that it is involved in oxygen detoxification in the anaerobe D. gigas.

Disruption and phenotypic analysis of six open reading frames from chromosome VII of Saccharomyces cerevisiae reveals one essential gene

Six open reading frames (ORFs) located on chromosome VII of Saccharomyces cerevisiae (YGR205w, YGR210c, YGR211w, YGR241c, YGR243w and YGR244c) were disrupted in two different genetic backgrounds using short-flanking homology (SFH) gene replacement. Sporulation and tetrad analysis showed that YGR211w, recently identified as the yeast ZPR1 gene, is an essential gene. The other five genes are non-essential, and no phenotypes could be associated to their inactivation. Two of these genes have recently been further characterized: YGR241c (YAP1802) encodes a yeast adaptor protein and YGR244c (LSC2) encodes the beta-subunit of the succinyl-CoA ligase. For each ORF, a replacement cassette with long flanking regions homologous to the target locus was cloned in pUG7, and the cognate wild-type gene was cloned in pRS416.

Cloning, sequencing and expression in the seeds and radicles of two Lupinus albus conglutin gamma genes

Two genes encoding conglutin gamma have been isolated from a Lupinus albus genomic library and sequenced. The expression of conglutin gamma was studied by partial amino acid sequencing of the mature seed protein and by nucleotide sequencing of reverse transcriptase-polymerase chain reaction products from various tissues during the plant life cycle.

A DNA fragment of Desulfovibrio gigas genome containing replication origin related genes

The nucleotide sequence of a 10,772 base pair (bp) region from Desulfovibrio gigas genome was determined. This sequence, which is adjacent to the region containing the coding units for the metalloproteins rubredoxin-oxygen oxidoreductase (ROO) and rubredoxin, includes the flavodoxin gene. Additionally, it also contains four open reading frames (ORFs) related to genes frequently found in replication origin regions of prokaryotes. These hypothetical encoded polypeptides are: the response regulator proteins (PhoP and PhoR) from the phosphate regulon, a DNA partitioning protein and an asparagine synthetase.

Analysis of the Desulfovibrio gigas transcriptional unit containing rubredoxin (rd) and rubredoxin-oxygen oxidoreductase (roo) genes and upstream ORFs

Rubredoxin-oxygen oxidoreductase, an 86-kDa homodimeric flavoprotein, is the final component of a soluble electron transfer chain that couples NADH oxidation with oxygen reduction to water from the sulfate-reducing bacterium Desulfovibrio gigas. A 4.2-kb fragment of D. gigas chromosomal DNA containing the roo gene and the rubredoxin gene was sequenced. Additional open reading frames designated as ORF-1, ORF-2, and ORF-3 were also identified in this DNA fragment. ORF-1 encodes a protein exhibiting homology to several proteins of the short-chain dehydrogenase/reductase family of enzymes. The N-terminal coenzyme-binding pattern and the active-site pattern characteristic of short chain dehydrogenase/reductase proteins are conserved in ORF-1 product. ORF-2 does not show any significant homology with any known protein, whereas ORF-3 encodes a protein having significant homologies with the branched-chain amino acid transporter AzlC protein family. Northern blot hybridization analysis with rd and roo-specific probes identified a common 1.5-kb transcript, indicating that these two genes are cotranscribed. The transcription start site was identified by primer extension analysis to be a guanidine 87 bp upstream the ATG start codon of rubredoxin. The transcript size indicates that the rd-roo mRNA terminates downstream the roo-coding unit. Putative -10 and -35 regulator regions of a sigma(70)-type promoter, having similarity with E. coli sigma(70) promoter elements, are found upstream the transcription start site. Rubredoxin-oxygen oxidoreductase and rubredoxin genes are shown to be constitutively and abundantly expressed. Using the data available from different prokaryotic genomes, the rubredoxin genomic organization and the first tentative to understand the phylogenetic relationships among the flavoprotein family are reported in this study.

Structure of a dioxygen reduction enzyme from Desulfovibrio gigas

Desulfovibrio gigas is a strict anaerobe that contains a well-characterized metabolic pathway that enables it to survive transient contacts with oxygen. The terminal enzyme in this pathway, rubredoxin:oxygen oxidoreductase (ROO) reduces oxygen to water in a direct and safe way. The 2.5 A resolution crystal structure of ROO shows that each monomer of this homodimeric enzyme consists of a novel combination of two domains, a flavodoxin-like domain and a Zn-beta-lactamase-like domain that contains a di-iron center for dioxygen reduction. This is the first structure of a member of a superfamily of enzymes widespread in strict and facultative anaerobes, indicating its broad physiological significance.

Differential expression of four genes encoding 1-aminocyclopropane-1-caroboxylate synthase in Lupinus albus during germination, and in response to indole-3-acetic acid and wounding

1-Aminocyclopropane-1-carboxylate (ACC) synthase (ACS; EC 4.4.1.14) is the key regulatory enzyme of the ethylene biosynthetic pathway and is encoded by a multigene family in Arabidopsis thaliana, tomato, mung bean and other plants. Southern blot analysis revealed the existence of at least five ACS genes in white lupin (Lupinus albus L.) genome. Four complete and one partial sequences representing different ACS genes were cloned from the lupin genomic library. The levels of expression of two of the genes, LA-ACS1 and LA-ACS3, were found to increase after hypocotyl wounding. Apparently, these two genes were up-regulated by exogenous IAA treatment of seedlings. The LA-ACS3 mRNA levels were also elevated in the apical part of hypocotyl, which is reported to contain a high endogenous auxin concentration. This gene may be involved in the auxin- and ethylene-controlled apical hook formation. The expression of the LA-ACS4 gene was found to be almost undetectable. This gene may represent a "silent" twin of LA-ACS5 as these two genes share a considerable level of homology in coding and non-coding regions. The LA-ACS5 mRNA is strongly up-regulated in the embryonic axis of germinating seeds at the time of radicle emergence, and was also found in roots and hypocotyls of lupin seedlings.

Molecular cloning of the gene encoding flavoredoxin, a flavoprotein from Desulfovibrio gigas

Sulfate-reducing bacteria are rich in unique redox proteins and electron carriers that participate in a variety of essential pathways. Several studies have been carried out to characterize these proteins, but the structure and function of many are poorly understood. Many Desulfovibrio species can grow using hydrogen as the sole energy source, indicating that the oxidation of hydrogen with sulfite as the terminal electron acceptor is an energy-conserving mechanism. Flavoredoxin is an FMN-binding protein isolated from the sulfate-reducing bacteria Desulfovibrio gigas that participates in the reduction of bisulfite from hydrogen. Here we report the cloning and sequencing of the flavoredoxin gene. The derived amino acid sequence exhibits similarity to several flavoproteins which are members of a new family of flavin reductases suggested to bind FMN in a novel mode.

Thermostabilization of proteins by diglycerol phosphate, a new compatible solute from the hyperthermophile Archaeoglobus fulgidus

Diglycerol phosphate accumulates under salt stress in the archaeon Archaeoglobus fulgidus (L. O. Martins, R. Huber, H. Huber, K. O. Stetter, M. S. da Costa, and H. Santos, Appl. Environ. Microbiol. 63:896-902, 1997). This solute was purified after extraction from the cell biomass. In addition, the optically active and the optically inactive (racemic) forms of the compound were synthesized, and the ability of the solute to act as a protecting agent against heating was tested on several proteins derived from mesophilic or hyperthermophilic sources. Diglycerol phosphate exerted a considerable stabilizing effect against heat inactivation of rabbit muscle lactate dehydrogenase, baker's yeast alcohol dehydrogenase, and Thermococcus litoralis glutamate dehydrogenase. Highly homologous and structurally well-characterized rubredoxins from Desulfovibrio gigas, Desulfovibrio desulfuricans (ATCC 27774), and Clostridium pasteurianum were also examined for their thermal stabilities in the presence or absence of diglycerol phosphate, glycerol, and inorganic phosphate. These proteins showed different intrinsic thermostabilities, with half-lives in the range of 30 to 100 min. Diglycerol phosphate exerted a strong protecting effect, with approximately a fourfold increase in the half-lives for the loss of the visible spectra of D. gigas and C. pasteurianum rubredoxins. In contrast, the stability of D. desulfuricans rubredoxin was not affected. These different behaviors are discussed in the light of the known structural features of rubredoxins. The data show that diglycerol phosphate is a potentially useful protein stabilizer in biotechnological applications.

The Lupinus albus class-III chitinase gene, IF3, is constitutively expressed in vegetative organs and developing seeds

A cDNA fragment encoding a Lupinus albus. L. class-III chitinase, IF3, was isolated, using a cDNA probe from Cucumis sativus L., by in-situ plaque hybridization from a cDNA library constructed in the Uni-ZAP XR vector, with mRNAs isolated from mature lupin leaves. The cDNA had a coding sequence of 293 amino acids including a 27-residue N-terminal signal peptide. A class-III chitinase gene was detected by Southern analysis in the L. albus genome. Western blotting experiments showed that the IF3 protein was constitutively present during seed development and in all the studied vegetative lupin organs (i.e., roots, hypocotyls and leaves) at two growth stages (7- and 20-d-old plants). Accumulation of both the IF3 mRNA and IF3 protein was triggered by salicylic acid treatment as well as by abiotic (UV-C light and wounding) and biotic stress conditions (Colletotrichum gloeosporioides infection). In necrotic leaves, IF3 chitinase mRNA was present at a higher level than that of another mRNA encoding a pathogenesis-related (PR) protein from L. albus (a PR-10) and that of the rRNAs. We suggest that one role of the IF3 chitinase could be in the defense of the plant against fungal infection, though our results do not exclude other functions for this protein.

Structure of Tetrahymena CCT theta gene and its expression under colchicine treatment

We report here the cloning and the characterization of the Tetrahymena pyriformis chaperonin-containing-TCP1 theta gene (TpCCT theta), an orthologue of the mouse chaperonin gene CCT theta. TpCCT theta gene is interrupted by eight introns, ranging in size between 91 and 419 nucleotides, and encodes a protein consisting of 540 amino acid residues (59.1 kDa), with a putative pI of 5.73. The amino acid sequence of TpCCT theta reveals 39.4-46.0% identity with the sequences of Candida albicans and mouse CCT theta subunits and 28.0-32.6% identity with the other TpCCT subunits known so far. We have studied the expression of this gene in exponentially growing Tetrahymena cells and in cells treated with colchicine for different times. The steady-state levels of CCT theta mRNA rapidly decrease in the first 30 min of colchicine treatment. Interestingly, treatment for subsequent 60 min gives expression levels higher than those found in exponentially growing cells.

Post-termination ribosome interactions with the 5'UTR modulate yeast mRNA stability

A novel form of post-transcriptional control is described. The 5' untranslated region (5'UTR) of the Saccharomyces cerevisiae gene encoding the AP1-like transcription factor Yap2 contains two upstream open reading frames (uORF1 and uORF2). The YAP2-type of uORF functions as a cis-acting element that attenuates gene expression at the level of mRNA turnover via termination-dependent decay. Release of post-termination ribosomes from the YAP2 5'UTR causes accelerated decay which is largely independent of the termination modulator gene UPF1. Both of the YAP2 uORFs contribute to the destabilization effect. A G/C-rich stop codon context, which seems to promote ribosome release, allows an uORF to act as a transferable 5'UTR-destabilizing element. Moreover, termination-dependent destabilization is potentiated by stable secondary structure 3' of the uORF stop codon. The potentiation of uORF-mediated destabilization is eliminated if the secondary structure is located further downstream of the uORF, and is also influenced by a modulatory mechanism involving eIF2. Destabilization is therefore linked to the kinetics of acquisition of reinitiation-competence by post-termination ribosomes in the 5'UTR. Our data explain the destabilizing properties of YAP2-type uORFs and also support a more general model for the mode of action of other known uORFs, such as those in the GCN4 mRNA.

The yeast transcription factor genes YAP1 and YAP2 are subject to differential control at the levels of both translation and mRNA stability

Two forms of post-transcriptional control direct differential expression of the Saccharomyces cerevisiae genes encoding the AP1-like transcription factors Yap1p and Yap2p. The mRNAs of these genes contain respectively one (YAP1 uORF) and two (YAP2 uORF1 and uORF2) upstream open reading frames. uORF-mediated modulation of post-termination events on the 5'-untranslated region (5'-UTR) directs differential control not only of translation but also of mRNA decay. Translational control is defined by two types of uORF function. The YAP1 -type uORF allows scanning 40S subunits to proceed via leaky scanning and re-initiation to the major ORF, whereas the YAP2 -type acts to block ribosomal scanning by promoting efficient termination. At the same time, the YAP2 uORFs define a new type of mRNA destabilizing element. Both post-termination ribosome scanning behaviour and mRNA decay are influenced by the coding sequence and mRNA context of the respective uORFs, including downstream elements. Our data indicate that release of post-termination ribosomes promotes largely upf -independent accelerated decay. It follows that translational termination on the 5'-UTR of a mature, non-aberrant yeast mRNA can trigger destabilization via a different pathway to that used to rid the cell of mRNAs containing premature stop codons. This route of control of non-aberrant mRNA decay influences the stress response in yeast. It is also potentially relevant to expression of the sizable number of eukaryotic mRNAs that are now recognized to contain uORFs.

Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions

Saccharomyces cerevisiae contains eight members of a novel and fungus-specific family of bZIP proteins that is defined by four atypical residues on the DNA-binding surface. Two of these proteins, Yap1 and Yap2, are transcriptional activators involved in pleiotropic drug resistance. Although initially described as AP-1 factors, at least four Yap proteins bind most efficiently to TTACTAA, a sequence that differs at position +/-2 from the optimal AP-1 site (TGACTCA); further, a Yap-like derivative of the AP-1 factor Gcn4 (A239Q S242F) binds efficiently to the Yap recognition sequence. Molecular modeling suggests that the Yap-specific residues make novel contacts and cause physical constraints at the +/-2 position that may account for the distinct DNA-binding specificities of Yap and AP-1 proteins. To various extents, Yap1, Yap2, Yap3, and Yap5 activate transcription from a promoter containing a Yap recognition site. Yap-dependent transcription is abolished in strains containing high levels of protein kinase A; in contrast, Gcn4 transcriptional activity is stimulated by protein kinase A. Interestingly, Yap1 transcriptional activity is stimulated by hydrogen peroxide, whereas Yap2 activity is stimulated by aminotriazole and cadmium. In addition, unlike other yap mutations tested, yap4 (cin5) mutations affect chromosome stability, and they suppress the cold-sensitive phenotype of yap1 mutant strains. Thus, members of the Yap family carry out overlapping but distinct biological functions.

Studies on the redox centers of the terminal oxidase from Desulfovibrio gigas and evidence for its interaction with rubredoxin

Rubredoxin-oxygen oxidoreductase (ROO) is the final component of a soluble electron transfer chain that couples NADH oxidation to oxygen consumption in the anaerobic sulfate reducer Desulfovibrio gigas. It is an 86-kDa homodimeric flavohemeprotein containing two FAD molecules, one mesoheme IX, and one Fe-uroporphyrin I per monomer, capable of fully reducing oxygen to water. EPR studies on the native enzyme reveal two components with g values at approximately 2.46, 2.29, and 1.89, which are assigned to low spin hemes and are similar to the EPR features of P-450 hemes, suggesting that ROO hemes have a cysteinyl axial ligation. At pH 7.6, the flavin redox transitions occur at 0 +/- 15 mV for the quinone/semiquinone couple and at -130 +/- 15 mV for the semiquinone/hydroquinone couple; the hemes reduction potential is -350 +/- 15 mV. Spectroscopic studies provided unequivocal evidence that the flavins are the electron acceptor centers from rubredoxin, and that their reduction proceed through an anionic semiquinone radical. The reaction with oxygen occurs in the flavin moiety. These data are strongly corroborated by the finding that rubredoxin and ROO are located in the same polycistronic unit of D. gigas genome. For the first time, a clear role for a rubredoxin in a sulfate-reducing bacterium is presented.

The third member of the Tetrahymena CCT subunit gene family, TpCCT alpha, encodes a component of the hetero-oligomeric chaperonin complex

The sequence of a third member of the Tetrahymena pyriformis chaperonin CCT ('chaperonin containing TCP1') subunit gene family is presented. This gene, designated TpCCT alpha, is the orthologue of the mouse chaperonin gene TCP1/CCT alpha. To characterize the CCT complex in this ciliate, we have produced polyclonal antibodies against synthetic peptides based on C-terminal sequences deduced from the primary sequences of the TpCCT alpha, TpCCT gamma and TpCCT eta subunits. We have also used polyclonal antibodies produced against recombinant yeast CCT alpha and CCT beta subunits. Using these antibodies, we show that Tetrahymena cells contain a hetero-oligomeric CCT chaperonin comprising at least seven distinct subunits. Three of these were assigned to specific TpCCT genes, whereas a fourth was recognized by the polyclonal antibody against yeast CCT beta, suggesting that this gene is also present in the ciliate. The CCT complex also contains other unidentified proteins that were recognized by the polyclonal antibody UM-1, raised against the putative ATP binding domain of the chaperonin proteins. TpCCT alpha gene expression was shown in exponentially growing cells and cells regenerating their cilia for different periods to have a similar pattern to the previously identified genes TpCCT gamma and TpCCT eta, and also to tubulin genes.

Constitutive flocculation in Saccharomyces cerevisiae through overexpression of the GTS1 gene, coding for a 'Glo'-type Zn-finger-containing protein

The product of the cloned GTS1 gene is characterized by structural features found in transcription factors. It contains one Zn-finger motif (CXXCX16CXXC) situated in the N-terminal end with a high degree of homology to the newly identified 'Glo' family of Zn-finger proteins (Ireland et al., 1994, EMBO J. 13, 3812-3821). The C-terminal end of the protein is characterized by poly (Ala-Gln) and poly-Gln stretches. Poly-Gln are part of trans-acting motifs in known transcription factors. Overexpression of the GTS1 gene results in constitutive flocculation. Whole cell electrophoretic mobility and hydrophobicity of GTS1 overexpressing cells was respectively lower and higher relative to control cells. GTS1-induced flocculation is hardly sensitive to mannose in contrast to FLO1-determined flocculation. Overexpression of the GTS1 gene in a flo1 background does not abolish flocculation, suggesting that the FLO1 gene is not linked with the GTS1 gene in a 'flocculation pathway'.

Analysis of a 17.9 kb region from Saccharomyces cerevisiae chromosome VII reveals the presence of eight open reading frames, including BRF1 (TFIIIB70) and GCN5 genes

We report the nucleotide sequence of a 17,893 bp DNA segment from the right arm of Saccharomyces cerevisiae chromosome VII. This fragment begins at 482 kb from the centromere. The sequence includes the BRF1 gene, encoding TFIIIB70, the 5' portion of the GCN5 gene, an open reading frame (ORF) previously identified as ORF MGA1, whose translation product shows similarity to heat-shock transcription factors and five new ORFs. Among these, YGR250 encodes a polypeptide that harbours a domain present in several polyA binding proteins. YGR245 is similar to a putative Schizosaccharomyces pombe gene, YGR248 shows significant similarity with three ORFs of S. cerevisiae situated on different chromosomes, while the remaining two ORFs, YGR247 and YGR251, do not show significant similarity to sequences present in databases.

Sequencing of a 9.9 kb segment on the right arm of yeast chromosome VII reveals four open reading frames, including PFK1, the gene coding for succinyl-CoA synthetase (beta-chain) and two ORFs sharing homology with ORFs of the yeast chromosome VIII

A 9.9 kb DNA fragment from the right arm of chromosome VII of Saccharomyces cerevisiae has been sequenced and analysed. The sequence contains four open reading frames (ORFs) longer than 100 amino acids. One gene, PFK1, has already been cloned and sequenced and the other one is the probable yeast gene coding for the beta-subunit of the succinyl-CoA synthetase. The two remaining ORFs share homology with the deduced amino acid sequence (and their physical arrangement is similar to that) of the YHR161c and YHR162w ORFs from chromosome VIII.

Characterization of a polyubiquitin gene in T. thermophila and of ubiquitin gene expression during sexual reproduction and under stress conditions

A 5-unit polyubiquitin gene, TTU3, was isolated from a T. thermophila genomic library and sequenced. This gene presents an extra triplet coding for Phe, a AGAGA motif and a putative HSE element in its 5'-non-coding region. The ubiquitin gene expression in this ciliate was investigated by Northern blot hybridization in conjugating cells or cells under stress conditions. Exponentially growing cells express two ubiquitin mRNAs of 0.75 and 1.8 kb and a new species of 1.4 kb is induced under hyperthermic stress. During sexual reproduction of the cells (conjugation) the 1.8-kb mRNA is still transcribed whereas the steady-state population of the 0.75 mRNA transcripts is strongly diminished. Southern blot analysis suggests that ubiquitin in T. thermophila constitutes a large family of about ten members.

Developmental expression and regulation by light of two closely related beta-tubulin genes in Lupinus albus

We present here the characterization of a Lupinus albus beta-tubulin gene, TubB2, which is closely related to TubB1. Both TubB1 and TubB2 transcripts are present in the embryonic axis of lupin dry seeds. The patterns of developmental expression of TubB1 and TubB2 beta-tubulin genes are strongly correlated. Both genes are expressed at higher levels in hypocotyls of 7-day-old etiolated plants compared to hypocotyls from plants grown under light/dark cycles. When etiolated plants are exposed to continuous white light, differential changes in the steady state levels of the TubB1 and TubB2 mRNAs from hypocotyls are observed. These changes are accompanied by an inhibition of hypocotyl extension.

The ABC transporter proteins Pat1 and Pat2 are required for import of long-chain fatty acids into peroxisomes of Saccharomyces cerevisiae

Peroxisomes of Saccharomyces cerevisiae are the exclusive site of fatty acid beta-oxidation. We have found that fatty acids reach the peroxisomal matrix via two independent pathways. The subcellular site of fatty acid activation varies with chain length of the substrate and dictates the pathway of substrate entry into peroxisomes. Medium-chain fatty acids are activated inside peroxisomes hby the acyl-CoA synthetase Faa2p. On the other hand, long-chain fatty acids are imported from the cytosolic pool of activated long-chain fatty acids via Pat1p and Pat2p, peroxisomal membrane proteins belonging to the ATP binding cassette transporter superfamily. Pat1p and Pat2p are the first examples of membrane proteins involved in metabolite transport across the peroxisomal membrane.

The Tetrahymena chaperonin subunit CCT eta gene is coexpressed with CCT gamma gene during cilia biogenesis and cell sexual reproduction

We report here the cloning and the characterization of the T. pyriformis CCT eta gene (TpCCT eta) and also a partial sequence of the corresponding T. thermophila gene (TtCCT eta). The TpCCt eta gene encodes a protein sharing a 60.3% identity with the mouse CCT eta. We have studied the expression of these genes in Tetrahymena exponentially growing cells, cells regenerating their cilia for different periods and during different stages of the cell sexual reproduction. These genes have similar patterns of expression to those of the previously identified TpCCt gamma gene. Indeed, the Tetrahymena CCT eta and CCT gamma genes are up-regulated at 60-120 min of cilia recovery, and in conjugation when vegetative growth was resumed and cell division took place. Our results seem to indicate that both CCT subunits play an important role in the biogenesis of the newly synthesized cilia of Tetrahymena and during its cell division.

Sequencing of a 17.6 kb segment on the right arm of yeast chromosome VII reveals 12 ORFs, including CCT, ADE3 and TR-I genes, homologues of the yeast PMT and EF1G genes, of the human and bacterial electron-transferring flavoproteins (beta-chain) and of the Escherichia coli phosphoserine phosphohydrolase, and five new ORFs

A 17.6 kb DNA fragment from the right arm of chromosome VII of Saccharomyces cerevisiae has been sequenced and analysed. The sequence contains twelve open reading frames (ORFs) longer than 100 amino acids. Three genes had already been cloned and sequenced: CCT, ADE3 and TR-I. Two ORFs are similar to other yeast genes: G7722 with the YAL023 (PMT2) and PMT1 genes, encoding two integral membrane proteins, and G7727 with the first half of the genes encoding elongation factors 1gamma, TEF3 and TEF4. Two other ORFs, G7742 and G7744, are most probably yeast orthologues of the human and Paracoccus denitrificans electron-transferring flavoproteins (beta chain) and of the Escherichia coli phosphoserine phosphohydrolase. The five remaining identified ORFs do not show detectable homology with other protein sequences deposited in data banks. The sequence has been deposited in the EMBL data library under Accession Number Z49133.

The complete sequence of a 9000 bp fragment of the right arm of Saccharomyces cerevisiae chromosome VII contains four previously unknown open reading frames

We report the sequence of a 9000 bp fragment from the right arm of Saccharomyces cerevisiae chromosome VII. Analysis of the sequence revealed four complete previously unknown open reading frames, which were named G7587, G7589, G7591 and G7594 following standard rules for provisional nomenclature. Outstanding features of some of these proteins were the homology of the putative protein coded by G7589 with proteins involved in transcription regulation and the transmembrane domains predicted in the putative protein coded by G7591.

A Tetrahymena orthologue of the mouse chaperonin subunit CCT gamma and its coexpression with tubulin during cilia recovery

A Tetrahymena pyriformis gene orthologue to the mouse CCT gamma gene has been cloned and sequenced. The coding region of this gene, named TpCCT gamma, is interrupted by six introns and codes for a protein of 559 amino acid residues. This protein shares a 57.6% identity with the mouse CCT gamma protein whereas in average a 30% identity was found with CCT alpha proteins from mammalian to yeast. The expression of this gene was investigated by Northern blot hybridization in Tetrahymena exponentially growing cells and cells during cilia recovery. The TpCCT gamma gene is expressed producing a unique transcript of 2.1 kilobases. A relevant aspect of our findings is the coordinated response of TpCCT gamma and tubulin genes to cilia regeneration. TpCCT gamma and tubulin transcripts reached higher levels between 45-120 min of reciliation compared to those found in exponentially growing cells. These high levels could be the result of the increase in apparent transcription rates detected at 60 min of reciliation. We also observed that TpCCT gamma transcripts are not increased after exposure of Tetrahymena cells to a heat-shock (28-->34 degrees C). Our results seem to indicate an important role of this gene in the differentiation process of ciliogenesis.

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.

The yeast YKL741 gene situated on the left arm of chromosome XI codes for a homologue of the human ALD protein

The yeast gene YKL741 is situated on the left arm of chromosome XI, 12 kb closer to the centromere with respect to the previously localized PAS1 gene. The new yeast gene codes for a homologue of the human ALD protein (ALD: adrenoleukodystrophy). The similarity between the YKL741 protein and the ALD protein is very high in the C-terminal half, which contains an ATP-binding cassette characteristic of the ABC family of transporters. Additionally the YKL741 protein shows some similarity to the ALD protein in the N-terminal half in three putative transmembrane spanning domains. The sequence has been deposited in the EMBL data library under Accession Number X76133 SC YKL.

Molecular cloning and sequence analysis of the gene of the molybdenum-containing aldehyde oxido-reductase of Desulfovibrio gigas. The deduced amino acid sequence shows similarity to xanthine dehydrogenase

In this report, we describe the isolation of a 4020-bp genomic PstI fragment of Desulfovibrio gigas harboring the aldehyde oxido-reductase gene. The aldehyde oxido-reductase gene spans 2718 bp of genomic DNA and codes for a protein with 906 residues. The protein sequence shows an average 52% (+/- 1.5%) similarity to xanthine dehydrogenase from different organisms. The codon usage of the aldehyde oxidoreductase is almost identical to a calculated codon usage of the Desulfovibrio bacteria.

Cloning and characterization of two ubiquitin::79-amino-acid extension protein-encoding fusion genes from Lupinus albus

Two different ubiquitin::79-amino-acid (aa) extension protein-encoding fusion genes were isolated from a Lupinus albus nuclear DNA library and sequenced. Both genes have 465-nucleotide open reading frames encoding a single ubiquitin (Ub) monomer fused in frame to a 79-aa extension (Ext) protein. The deduced aa sequences of the encoded Ub are identical to the aa sequences of Ub from other plants. The encoded Ext proteins are putative ribosomal proteins, highly basic, differing by 2 aa from each other, and have a high degree of similarity to Ext proteins from other plants.

Overexpression of YAP2, coding for a new yAP protein, and YAP1 in Saccharomyces cerevisiae alleviates growth inhibition caused by 1,10-phenanthroline

A new member of the yeast yAP family, designated YAP2, has been isolated and characterized. The protein displays a high homology with the DNA-binding domain of yAP-1, which contains a basic DNA-binding domain and leucine zipper motif and binds in vitro to the same cis-element. Growth arrest of yeast caused by low concentrations of 1,10-phenanthroline, resulting in zinc and/or iron deprivation, is overcome by over-expression of YAP1 or YAP2. In fact, yeast cells over-expressing YAP1 or YAP2 display pleiotropic drug resistance. On the other hand, a yap2 null mutant has an increased thermotolerance under starvation conditions caused by 1,10-phenanthroline. The latter mutant might become an excellent tool in the study of pathways leading toward thermotolerance acquisition.

Clusters of 5S rRNAs in the intergenic region of ubiquitin genes in Tetrahymena pyriformis

Here, we report the molecular analysis of two independent 5S rRNA clusters found in the intergenic region of two ubiquitin genomic clones isolated from Tetrahymena pyriformis. Each cluster contains two 120-bp-long coding regions organized in tandem with 142/145-bp-long spacers.

Heat-shock-induced protein synthesis is responsible for the switch-off of hsp70 transcription in Tetrahymena

We had previously described that new RNA synthesis is required for expression of the heat shock protein HSP70. Here, we find that the HSP70 mRNA decreases its levels under stress conditions, heat shock (HS) or arsenite (As), and that its levels start to decline at the same time as maximal HSPs synthesis (including HSP70) occurs. This suggests that regulation of the hsp70 gene is mainly exerted at the transcriptional level. Accumulation of the HSP70 mRNA in cells stressed in presence of cycloheximide (CHX), indicates that (a) protein(s) non-existent before stress, possibly HSP70 itself (which is shown here to be relatively stable), is involved in negatively regulating hsp70 expression. Since degradation of the HSP70 mRNA is also shown to occur in cells heat-shocked under CHX, as seen from decay of its levels upon addition of actinomycin D (AMD), the protein(s) must repress hsp70 expression at the transcriptional level. Other conditions that affect normal protein synthesis, namely the translation inhibitor puromycin and the arginine-analog canavanine (shown here to be stress inducers in Tetrahymena pyriformis), also cause a delay in transcription-arrest of the HSP70 mRNA. Under severe stress conditions of HS (36 degrees C) or As (350 microM), the levels of HSP70 mRNA are higher than under mild stress conditions, however, no significant difference is seen in the pattern of HSP70 mRNA decay.

The mechanisms of tubulin messenger regulation during Tetrahymena pyriformis reciliation

The reciliation of Tetrahymena pyriformis cells is accompanied in the first minutes by a transient induction of stress mRNAs, i.e. hsp70 and ubiquitin. At the same time an accentuated and coordinate reduction in the amount of alpha- and beta-tubulin mRNAs is observed as analyzed by Northern blot hybridization using the homologous genomic tubulin probes. Between 60 and 120 min after the onset of reciliation, tubulin transcripts in the cytoplasm reach higher values than in exponentially growing cells. Run-on transcription assays reveal that the decrease in tubulin mRNA levels is not caused by a decrease in transcription of tubulin genes. The results obtained show that the apparent tubulin gene transcription rate is increased in reciliating cells from 15 min up to 90 min. The block of transcription using actinomycin D shows that hsps are not implicated in the destabilization of tubulin mRNA during the first minutes of reciliation. The effects of the inhibitors of protein synthesis, cycloheximide and pactamycin, on tubulin mRNA levels suggest that the translational apparatus plays a role in the stability of tubulin mRNA in cells reciliating for 15 and 30 min. Experiments using the microtubule-polymerizing drug taxol also show that tubulin mRNA destabilization is not a simple consequence of a temporary increase in free tubulin subunit pools resulting from cilia resorption.

Molecular cloning and sequencing analysis of a beta-tubulin gene from Lupinus albus

Genomic lambda-Dash library constructed from Lupinus albus nuclear DNA was screened using a fragment of the beta-tubulin cDNA (beta 8-31) clone of Chlamydomonas reinhardtii as probe. One of the positive recombinant phages was isolated, subcloned and analysed by sequencing. We present here nucleotide and derived amino acid sequences of the beta-tubulin gene, designated as L beta 1 and identified by similarity with other beta-tubulins. The L beta 1-encoded protein reveals a very high degree of similarity with other plant tubulins and contains consensus sequences for binding guanine base, phosphate and Mg2+. Northern analysis of total RNA isolated from roots, leaves, flowers and pools revealed that Lupinus albus beta-tubulin genes are constitutively expressed in all studied plant tissues.

Known heat-shock proteins are not responsible for stress-induced rapid degradation of ribosomal protein mRNAs in yeast

We have previously shown that the heat-induced enhanced decay of yeast mRNAs encoding ribosomal proteins (rp-mRNAs) requires ongoing transcription during the heat treatment [Herruer et al. (1988) Nucl. Acids Res. 16, 7917]. In order to determine whether this requirement reflects the need for heat-shock protein (hsp), we analysed the effect of heat shock on rp-mRNA levels in several yeast strains in which each of the heat-shock genes encoding hsp26, hsp35 or hsp83 had been individually disrupted. In all three strains we still observed increased degradation of rp-mRNAs immediately after the temperature shift, demonstrating that hsp26, hsp35 and hsp83 are not required for this effect. Accelerated turnover of rp-mRNA was also found to occur upon raising the growth temperature of a mutant strain that contains a disruption of the gene specifying the heat-shock transcription factor and in wild-type yeast cells treated with canavanine, an arginine analogue that will be incorporated into all known hsps and that is known to cause misfolding of the polypeptide chain. Latter observation suggests that enhanced rp-mRNA decay is a more general stress-related phenomenon. Taken together, these data strongly indicate that the trans-acting factor required for the increase in the rate of degradation of rp-mRNAs upon stress is not one of the known yeast hsps.

Molecular cloning and expression of a Tetrahymena pyriformis ubiquitin fusion gene coding for a 53-amino-acid extension protein

The genome of Tetrahymena pyriformis has been shown to contain a ubiquitin multigene family consisting of several polyubiquitin genes and at least one ubiquitin fusion gene. We report here the isolation and characterization of one genomic clone (pTU11), that encodes a ubiquitin extension protein. A comparison of the predicted amino acid sequence of the ubiquitin extension protein gene of T. pyriformis with those from other organisms indicated a high degree of homology. However, the Tetrahymena ubiquitin extension protein contains 53 and not 52 amino acids. This feature is different from all ubiquitin 52-amino-acid extension protein genes thus far sequenced. Furthermore, we found an array of four cysteine residues similar to those found in nucleic acid binding proteins. Also, the C-terminal sequence possesses a conserved motif which may represent a nuclear translocation signal. The ubiquitin 53-amino-acid extension protein gene encodes the smallest class of ubiquitin mRNAs in T. pyriformis.

Different patterns of expression of beta-tubulin genes in Tetrahymena pyriformis during reciliation

The ciliate Tetrahymena pyriformis contains one alpha-tubulin (alpha TT) and two beta-tubulin (beta TT1 and beta TT2) genes. The specific expression of these genes was investigated by Northern blot hybridization using oligonucleotide probes complementary to beta TT1 and beta TT2 genes and the coding region of the alpha-tubulin gene. The three genes are expressed producing 1.8-kb mRNAs but the level of beta TT1 mRNA is much higher than that of beta TT2 mRNA. During cilia regeneration, we found that the expression patterns of the alpha TT and beta TT1 genes are similar whereas that of the beta TT2 gene is different. The alpha TT and beta TT1 transcripts reached higher values between 60-120 min after the onset of reciliation than in exponentially growing cells, while beta TT2 transcripts were maintained at low levels during the whole period. The differences in the amounts of steady-state populations of the both beta-tubulin mRNAs do not correspond to the copy number per haploid genome. These differences could result from the fact that the promoter region of beta TT2 may contain highly structured sequences which would affect the binding of the respective trans-acting factor(s). The apparent transcription rate revealed a significant increase at 15 min of reciliation which could be responsible for the high levels of alpha TT and beta TT1 transcripts in the cytoplasm between 60-120 min of reciliation. This coordinated response to cilia regeneration of the alpha TT and beta TT1 tubulin genes is also a relevant aspect of our findings. Several conserved motifs found in their promoter regions led us to think that some of them may function as cis-elements in the specific binding of nuclear protein factor(s).

Multiple alpha-tubulin isoforms in cilia and cytoskeleton of Tetrahymena pyriformis generated by post-translational modifications. Studies during reciliation

alpha-Tubulin microheterogeneity was studied in Tetrahymena pyriformis. Using two-dimensional electrophoretic analysis, we found between five and seven alpha-tubulin and four beta-tubulin isoforms in cilia and four or five alpha-tubulins and two beta-tubulins in cytoskeleton. Immunoblotting assay with anti-(acetyl alpha-tubulin) monoclonal antibody 6-11B-1 and [3H]acetate labelling revealed that the alpha-tubulin isoforms are post-translationally modified by acetylation. Our results also show that tubulins in the soluble cytoplasmic fraction are not acetylated. Nevertheless, a slight reaction with the antibody 6-11 B-1 can be observed in the taxol and vinblastine-treated cytoplasmic pool. Pulse/chase experiments using [35S]methionine during cell reciliation have demonstrated that the basic alpha-tubulin isoforms are converted into acidic isoforms in the absence of protein synthesis, suggesting that the basic alpha-tubulin is the precursor of the acidic forms which are found in cilia and cytoskeleton. In-vivo-translation selection demonstrated the existence of a single precursor molecule which corresponded to the most basic alpha-tubulin. Taken together, our results provide evidence for the existence of post-translational modifications, namely acetylation. Nevertheless, other post-translational mechanisms involved in the biosynthesis of microtubules of cilia and cytoskeleton are required to explain the whole alpha-tubulin heterogeneity.

The macronuclear polyubiquitin gene of the ciliate Tetrahymena pyriformis

The presence of ubiquitin in ciliates was first demonstrated in Tetrahymena pyriformis. One clone--pTU2--presents two incomplete open reading frames and the putative polyubiquitin genes have been shown to be highly similar to those of other organisms. To further analyze the organization of this multigene family, several fragments of macronuclear DNA were cloned. We report here the isolation and characterization of one genomic clone (pTU20) that encodes a polyubiquitin gene (TU20) with five tandem repeats and presenting only one extra triplet CAA (Gln) upstream from the TGA. The promoter region of TU20 also presents a consensus heat shock element. The specific detection of RNA species with a synthetic oligonucleotide probe reveals that it corresponds to the 1.8 kb mRNA species whose expression is increased by temperature stress.

Properties and partial characterization of the heat-shock factor from Tetrahymena pyriformis

A heat-shock-factor-binding activity was identified in Tetrahymena pyriformis whole-cell extracts and was further purified by sequential heparin-agarose and sequence-specific oligonucleotide affinity chromatography. Tetrahymena heat-shock factor (HSF) was able to bind to the heat-shock elements (HSE) both before and after thermal stress, although heat shock altered both the HSE-binding affinity and the protein.DNA-complex mobility on polyacrylamide gels. The mobility difference was significantly reduced by treatment of the proteins with phosphatase. The HSE-binding proteins, isolated by oligonucleotide-affinity chromatography, migrated on SDS/polyacrylamide gels as a closely spaced doublet to about 70 kDa. Polypeptides with similar molecular mass were recovered from preparative band-shift gels indicating that both are components of the protein.DNA complex.

Methylated amino acids in the proteins of the cytoplasmic ribosome of Tetrahymena thermophila

Two-dimensional electrophoretic analysis of proteins of the cytoplasmic ribosome of the protozoa Tetrahymena thermophila labeled in vivo with L-[14C1]methionine and L-[3H-methyl]methionine identifies one heavily methylated protein in each ribosomal subunit. These proteins, S31 and L21, each contain N epsilon-trimethyl-lysine.

Ubiquitin genes in Tetrahymena pyriformis and their expression during heat shock

The genome of Tetrahymena pyriformis was shown to contain a ubiquitin multigene family consisting of at least four polyubiquitin genes. Three genomic clones with different ubiquitin-coding sequences, were isolated and partially characterized. The complete nucleotide sequence of one of these clones (pTU2) was determined and showed two open reading frames (ORFs) at opposite ends of the cloned DNA insert. A comparison of the predicted amino acid (aa) sequence of T. pyriformis ubiquitin-coding unit with those from other organisms indicated a high degree of homology. However, Tetrahymena ubiquitin contained two aa substitutions at positions 16 (Asp) and 19 (Ala). Interestingly, the first pTU2 ORF showed two extra triplets coding for Ser and Gln, upstream from TGA. This feature is different from all the polyubiquitin genes thus far sequenced. Regions flanking the 3' and 5' ubiquitin-coding sequences presented several conserved motifs. The 5' flanking sequence of the second ORF of pTU2 contained one heat-shock element. We therefore studied the expression of the ubiquitin genes under stress conditions. The results showed that they are heat-inducible and that a new specific 1.6-kb mRNA appeared. These results suggest that the regulation of ubiquitin genes is important in T. pyriformis under thermal stress conditions.

Association of African swine fever virus with the cytoskeleton

The association of African swine fever virus (ASFV) with the cytoskeleton was investigated. Immunofluorescent studies of ASFV infected cells with anti-ASFV serum showed a temporal and spatial development of viral inclusions which moved from a peripheral to a perinuclear location and fused to give a single large perinuclear factory. The migration and fusion of viral inclusions was inhibited by colchicine suggesting a function for microtubules in assembly site organization not previously described. Accumulation of virions outside the inclusions and inhibition of viral release was also observed in colchicine treated cells. Viral antigens and structural elements were retained on the cytoskeleton fraction of Triton X-100 extracted cells. Reorganization of cytoskeletal elements around the assembly sites was demonstrated by transmission electronmicroscopy and by immunofluorescent studies using monoclonal antibodies against actin, tubulin and vimentin. Intermediate filaments accumulated around the viral factories, microtubules were greatly decreased in number and microfilaments were reorganized in association with the plasma membrane. Bundles of 15 nm tubules of unknown origin were also observed around the assembly sites. The distribution of viral proteins in soluble, cytoskeleton and detergent insoluble nuclear fractions was studied by pulse-chase experiments with [35S]methionine. SDS-PAGE analysis showed the presence in the cytoskeletal and nuclear fractions of 150, 72, 38, 28, 19 and 15 kDa virus structural proteins which increased after a 5 h chase. Our results indicate a close association of ASFV replication with the cytoskeleton similar to events described during FV3 replication but which differ from those occurring in poxvirus-infected cells.

Destabilization of tubulin mRNA during heat shock in Tetrahymena pyriformis

The regulation of tubulin gene expression was studied in Tetrahymena pyriformis cells during heat shock (shift from 28 degrees C to 34 degrees C). Fluorograms of two-dimensional gels of radiolabelled proteins synthesized during thermal stress revealed that tubulin synthesis is highly repressed when compared with that of exponentially growing cells. The variation in the levels of alpha and beta-tubulin mRNAs was analyzed by Northern-blot hybridization using homologous genomic probes (alpha TT and beta TT1). The results obtained show that heat shock induces a drastic and coordinate reduction in the amount of alpha and beta-tubulin mRNAs isolated from polysomes. This decrease is not due to a shift from the polysomes to the post-polysomal fraction because it was also observed when total cytoplasmic mRNAs were analyzed. Run-on transcription experiments were performed in order to examine whether repression of transcription in heat-shocked cells could explain that reduction. The results obtained show that the apparent rates of tubulin gene transcription are not significantly modified, but on the contrary increase slightly in cells heat-shocked for 15 min and 30 min. The effects of inhibitors of protein synthesis, cycloheximide and pactamycin, on the destabilization of tubulin mRNAs were tested in heat-shocked Tetrahymena cells. Our results revealed that in the presence of these inhibitors, tubulin mRNAs become more stable thus suggesting that an induced factor may be involved in the degradation of alpha and beta-tubulin mRNAs during heat shock.