Characterization of a fission yeast SUMO-1 homologue, pmt3p, required for multiple nuclear events, including the control of telomere length and chromosome segregation.

Unlike ubiquitin, the ubiquitin-like protein modifier SUMO-1 and its budding yeast homologue Smt3p have been shown to be more important for posttranslational protein modification than for protein degradation. Here we describe the identification of the SUMO-1 homologue of fission yeast, which we show to be required for a number of nuclear events including the control of telomere length and chromosome segregation. A disruption of the pmt3(+) gene, the Schizosaccharomyces pombe homologue of SMT3, was not lethal, but mutant cells carrying the disrupted gene grew more slowly. The pmt3Delta cells showed various phenotypes such as aberrant mitosis, sensitivity to various reagents, and high-frequency loss of minichromosomes. Interestingly, we found that pmt3(+) is required for telomere length maintenance. Loss of Pmt3p function caused a striking increase in telomere length. When Pmt3p synthesis was restored, the telomeres became gradually shorter. This is the first demonstration of involvement of one of the Smt3p/SUMO-1 family proteins in telomere length maintenance. Fusion of Pmt3p to green fluorescent protein (GFP) showed that Pmt3p was predominantly localized as intense spots in the nucleus. One of the spots was shown to correspond to the spindle pole body (SPB). During prometaphase- and metaphase, the bright GFP signals at the SPB disappeared. These observations suggest that Pmt3p is required for kinetochore and/or SPB functions involved in chromosome segregation. The multiple functions of Pmt3p described here suggest that several nuclear proteins are regulated by Pmt3p conjugation.

Genetic and biochemical analysis of the adenylyl cyclase-associated protein, cap, in Schizosaccharomyces pombe.

We have identified, cloned, and studied a gene, cap, encoding a protein that is associated with adenylyl cyclase in the fission yeast Schizosaccharomyces pombe. This protein shares significant sequence homology with the adenylyl cyclase-associated CAP protein in the yeast Saccharomyces cerevisiae. CAP is a bifunctional protein; the N-terminal domain appears to be involved in cellular responsiveness to RAS, whereas loss of the C-terminal portion is associated with morphological and nutritional defects. S. pombe cap can suppress phenotypes associated with deletion of the C-terminal CAP domain in S. cerevisiae but does not suppress phenotypes associated with deletion of the N-terminal domain. Analysis of cap disruptants also mapped the function of cap to two domains. The functional loss of the C-terminal region of S. pombe cap results in abnormal cellular morphology, slow growth, and failure to grow at 37 degrees C. Increases in mating and sporulation were observed when the entire gene was disrupted. Overproduction of both cap and adenylyl cyclase results in highly elongated large cells that are sterile and have measurably higher levels of adenylyl cyclase activity. Our results indicate that cap is required for the proper function of S. pombe adenylyl cyclase but that the C-terminal domain of cap has other functions that are shared with the C-terminal domain of S. cerevisiae CAP.

Isolation of a novel gene, moc2, encoding a putative RNA helicase as a suppressor of sterile strains in Schizosaccharomyces pombe.

A novel gene designated moc2, which encodes a putative RNA helicase, was isolated from Schizosaccharomyces pombe on the basis of its suppression of the sterility of two different mutant strains, one of which had elevated levels of cAMP and the other deregulated Ras functioning as a result of an ectopic expression of dominant negative RAS2. Moc2 is highly homologous to the RNA helicase DED1 of Saccharomyces cerevisiae (58% identity) and PL10 of mouse (50% identity). Disruption of the moc2 gene indicated that moc2 is essential for cell growth. The moc2 gene seems to have roles in both sexual differentiation and cell growth.

Regulation of glpD and glpE gene expression by a cyclic AMP-cAMP receptor protein (cAMP-CRP) complex in Escherichia coli.

The glpE gene of E. coli was found to be transcribed divergently with respect to glpD, which is adjacent to glpE head-to-head on the E. coli chromosome. We constructed glpD- and/or glpE-lacZ fusion plasmids, which provided glpD and lacZ as reporter genes. The expression of glpD and glpE, under the control of the cAMP-CRP complex, was examined by measuring the activities in E. coli cells of beta-galactosidase encoded by lacZ and glycerol-3-phosphate dehydrogenase encoded by glpD. In the double-reporter-gene system, the expression of glpD and glpE was found to be positively regulated by cAMP-CRP. We also confirmed that intracellular levels of the translation products and the transcripts from glpD and glpE were positively regulated by cAMP-CRP. The cAMP-mediated induction of gene expression of glpD and glpE was significantly affected by structural alterations of the single CRP-binding site between glpD and glpE. These results indicate that the single CRP-binding site is a cis-acting element involved in the positive regulation of the expression of both glpD and glpE at the transcriptional level.

Identification of the GGPS1 genes encoding geranylgeranyl diphosphate synthases from mouse and human.

E,E,E-Geranylgeranyl diphosphate (GGPP) is an important precursor of carotenoids and geranylgeranylated proteins such as small G proteins. In this study, we have identified mouse and human GGPP synthase genes. Sequence analysis showed that mouse and human GGPP synthases share a high level of amino acid identity (94%) with each other, and share a high level of similarity (45-50%) with GGPP synthases of lower eukaryotes, but only weak similarity (22-31%) to plant and prokaryotic GGPP synthases. Both of the newly identified GGPP synthase genes from mouse and human were expressed in Escherichia coli, and their gene products displayed GGPP synthase activity when isopentenyl diphosphate and farnesyl diphosphate were used as substrates. The GGPP synthase activity of these genes was also confirmed by demonstrating carotenoid synthesis after co-transformation of E. coli with a plasmid expressing the crt genes derived from Erwinia uredovora, and a plasmid expressing either the mouse or human GGPS1 gene. Southern blot analysis suggests that the human GGPS1 gene is a single copy gene.

Polyprenyl diphosphate synthase essentially defines the length of the side chain of ubiquinone.

Ubiquinone, known as a component of the electron transfer system in many organisms, has a different length of the isoprenoid side chain depending on the species, e.g., Escherichia coli, Saccharomyces cerevisiae and humans have 8, 6, and 10 isoprene units in the side chain, respectively. No direct evidence has yet shown what factors define the length of the side chain of ubiquinone. Here we proved that the polyprenyl diphosphate that was available in cells determined the length of the side chain of ubiquinone. E. coli octaprenyl diphosphate synthase (IspB) was expressed with the mitochondrial import signal in S. cerevisiae. Such cells produced ubiquinone-8 in addition to the originally existing ubiquinone-6. When IspB was expressed in a S. cerevisiae COQ1 defective strain. IspB complemented the defect of the growth on the non-fermentable carbon source. Those cells had the activity of octaprenyl diphosphate synthase and produced only ubiquinone-8. These results opened the possibility of producing the type of ubiquinone that we need in S. cerevisiae simply by expressing the corresponding polyprenyl diphosphate synthase.

Biological significance of the side chain length of ubiquinone in Saccharomyces cerevisiae.

Ubiquinone (UQ), an important component of the electron transfer system, is constituted of a quinone structure and a side chain isoprenoid. The side chain length of UQ differs between microorganisms, and this difference has been used for taxonomic study. In this study, we have addressed the importance of the length of the side chain of UQ for cells, and examined the effect of chain length by producing UQs with isoprenoid chain lengths between 5 and 10 in Saccharomyces cerevisiae. To make the different UQ species, different types of prenyl diphosphate synthases were expressed in a S. cerevisiae COQ1 mutant defective for hexaprenyl diphosphate synthesis. As a result, we found that the original species of UQ (in this case UQ-6) had maximum functionality. However, we found that other species of UQ could replace UQ-6. Thus a broad spectrum of different UQ species are biologically functional in yeast cells, although cells seem to display a preference for their own particular type of UQ.

Molecular cloning and sequencing of the glycogen phosphorylase gene from Escherichia coli.

The glgP gene, which codes for glycogen phosphorylase, was cloned from a genomic library of Escherichia coli. The nucleotide sequence of the glgP gene contained a single open reading frame encoding a protein consisting of 790 amino acid residues. The glgP gene product, a polypeptide of Mr 87,000, was confirmed by SDS-polyacrylamide gel electrophoresis. The deduced amino acid sequence showed that homology between glgP of E. coli and rabbit glgP, human glgP, potato glgP, and E. coli malP was 48.6, 48.6, 42.3, and 46.1%, respectively. Within this homologous region, the active site, glycogen storage site, and pyridoxal-5'-phosphate binding site are well conserved. The enzyme activity of glycogen phosphorylase increased after introduction on a multicopy of the glgP gene.

Functional analysis of the fic gene involved in regulation of cell division.

We have shown that cAMP may be a regulation factor in cell division of Escherichia coli (Utsumi et al., 1982, 1989). The fic (filamentation induced by cAMP) gene of this system found previously (Utsumi, et al., 1982) was analysed in this study. The open reading frame of the fic gene coded for 200 amino acids. The pabA (p-aminobenzoate synthase) gene was found downstream from the fic gene. The distance between the end of fic and the start of pabA was 31 base pairs. To deduce the function of Fic protein, the fic gene was destroyed by the kanamycin-resistant (Kmr) gene and the fic gene was shown to be essential for growth of E. coli. Such mutants required PAB (p-aminobenzoate) or folate for growth. These data suggested that the Fic protein is involved in the synthesis of PAB or folate and the fic gene could be part of a pab operon. In cells starved of them, cell division was inhibited. Addition of folate also repressed the filamentation induced by cAMP at 43 degrees C in the fic-1 mutant. These results would indicate that Fic protein and cAMP are involved in a new regulatory mechanism of cell division via folate metabolism. Furthermore, it is also shown that cell division could be controlled by coordination of cAMP, Fic and Fts proteins.

Analysis of the decaprenyl diphosphate synthase (dps) gene in fission yeast suggests a role of ubiquinone as an antioxidant.

Schizosaccharomyces pombe produces ubiquinone-10 whose side chain is thought to be provided by the product generated by decaprenyl diphosphate synthase. To understand the mechanism of ubiquinone biosynthesis in S. pombe, we have cloned the gene encoding decaprenyl diphosphate synthase by the combination of PCR amplification of the fragment and subsequent library screening. The determined DNA sequence of the cloned gene, called dps, revealed that the dps gene encodes a 378-amino-acid protein that has the typical conserved regions observed in many polyprenyl diphosphate synthases. Computer-assisted homology search indicated that Dps is 45 and 33% identical with hexaprenyl diphosphate synthase from Saccharomyces cerevisiae and octaprenyl diphosphate synthase from Escherichia coli, respectively. An S. pombe dps-deficient strain was constructed. This disruptant was not able to synthesize ubiquinone and had no detectable decaprenyl diphosphate synthase activity, indicating that the dps gene is unique and responsible for ubiquinone biosynthesis. The S. pombe dps-deficient strain could not grow on either rich medium supplemented with glycerol or on minimal medium supplemented with glucose. The dps-deficient strain required cysteine or glutathione for full growth on the minimal medium. In addition, the dps-deficient strain is more sensitive to H2O2 and Cu2+ than the wild type. These results suggests a role of ubiquinone as an antioxidant in fission yeast cells.

Stationary phase-specific expression of the fic gene in Escherichia coli K-12 is controlled by the rpoS gene product (sigma 38).

The fic gene, near pabA located at 75 min of the Escherichia coli chromosome, was previously identified as the regulatory factor of cell division. In this paper we have examined how fic gene expression is controlled during the growth cycle using a fic-lacZ protein fusion plasmid (pFL1). Its expression was induced at stationary phase while it was nearly abolished in rpoSmutants. Using a RNase protection assay, fic transcript at stationary phase was detected in rpoS+ strains, but not in the rpoS mutants. Furthermore, primer extension analysis indicated that the fic transcript controlled by RpoS initiates at a G located 185 bp upstream from ATG of the fic coding region. Compared with the sigma 70 recognition sequence, the -10 region of fic promoter resembled the Pribnow box, but no homologous sequence was observed at the -35 region. These results were consistent with the characteristic sequence profile of fic promoter recognized specifically by RpoS in vitro, which is the only example of the type III promoter so far detected in vitro and in vivo.

Effects of the Escherichia coli sfsA gene on mal genes expression and a DNA binding activity of SfsA.

The sfsA gene was identified as one of the sfs genes the over-expression of which stimulates maltose fermentation of the Mal- Escherichia coli strain MK2001 (crp*1, cya:Km(r)). Expression from the malPQ promoter, which was measured using a chromosomally integrated malPp-lacZ fusion, was induced by over-expressing the sfsA gene in the crp*1, cya:Km(r) strain. The level of the MalE protein was increased in crp*1, cya:Km(r) cells over-producing SfsA. The SfsA protein was purified to homogeneity and tested for DNA binding activity. The purified SfsA protein binds to DNA non-specifically. All these results may suggest that SfsA functions as a DNA binding protein to induce the mal genes in coordination with CRP*1.

Cloning and promoter analysis of the Escherichia coli adenylate cyclase gene.

The gene for adenylate cyclase of E. coli has been cloned in the plasmid pBR322. The Cya- strain transformed with the isolated plasmids produces significant amounts of adenylate cyclase and cAMP. Some of the Cya+ plasmids were shown to direct the synthesis of a 85,000 dalton polypeptide in a cell-free system. The direction of transcription and the location of the cya promoter including the transcriptional start site were determined by an S1 digestion method. DNA sequence around the promoter region indicates that a putative coding region for adenylate cyclase begins at +233. The 233 bp leader region could encode a potential small polypeptide containing 30 amino acids. Two probable CRP binding sites were found in the leader region, suggesting a negative control at the transcriptional level by CRP-cAMP.

Control mechanism of the Escherichia coli K-12 cell cycle is triggered by the cyclic AMP-cyclic AMP receptor protein complex.

The role of cyclic AMP (cAMP) in the cell cycle of Escherichia coli K-12 was studied in three mutant strains. One was KI1812, in which the cya promoter is replaced by the lacUV5 promoter. In KI1812, isopropyl-beta-D-thiogalactopyranoside induced the synthesis of cya mRNA, and at the same time cell division was inhibited and short filaments containing multiple nuclei were formed. The other strains were constructed as double mutants (NC6707 cya sulB [ftsZ(Ts)] and TR3318 crp sulB [ftsZ(Ts)]). In both double mutants, filamentation was repressed at 42 degrees C, but it was induced again by addition of cAMP in strain NC6707 and introduction of pHA7 containing wild-type crp in TR3318. These results indicate that lateral wall synthesis in the E. coli cell cycle is triggered by the cAMP-cAMP receptor protein complex.

Genetic and biochemical analysis of the adenylyl cyclase of Schizosaccharomyces pombe.

The adenylyl cyclase gene, cyr1, of Schizosaccharomyces pombe has been cloned. We have begun an analysis of the function and regulation of adenylyl cyclase by disrupting this gene and by over-expressing all or parts of this gene in various strains. cyr1- strains are viable and contain no measurable cyclic AMP. They conjugate and sporulate under conditions that normally inhibit wild-type strains. Strains containing the cyr1 coding sequences transcribed from the strong adh1 promoter contain greatly elevated adenylyl cyclase activity, as measured in vitro, but only modestly elevated cAMP levels. Such strains conjugate and sporulate less frequently than wild-type cells upon nutrient limitation. Strains which carry the wild-type cyr1 gene but that also express high levels of the amino terminal domain of adenylyl cyclase behave much like cyr1-strains, suggesting that the amino terminal domain can bind a positive regulator. A protein that copurifies with the adenylyl cyclase of S. pombe cross-reacts to antiserum raised against the S. cerevisiae adenylyl cyclase-associated regulatory protein, CAP.

Nucleotide sequences of fic and fic-1 genes involved in cell filamentation induced by cyclic AMP in Escherichia coli.

The nucleotide sequences of fic-1 involved in the cell filamentation induced by cyclic AMP in Escherichia coli and its normal counterpart fic were analyzed. The open reading frame of both fic-1 and fic coded for 200 amino acids. The Gly at position 55 in the Fic protein was changed to Arg in the Fic-1 protein. The promoter activity of fic was confirmed by fusing fic and lacZ. The gene downstream from fic was found to be pabA (p-aminobenzoate). There is an open reading frame (ORF190) coding for 190 amino acids upstream from the fic gene. Computer-assisted analysis showed that Fic has sequence similarity with part of CDC28 of Saccharomyces cerevisiae, CDC2 of Schizosaccharomyces pombe, and FtsA of E. coli. In addition, ORF190 has sequence similarity with the cyclosporin A-binding protein cyclophilin.

Cloning and sequencing of an Escherichia coli gene, nlp, highly homologous to the ner genes of bacteriophages Mu and D108.

An nlp (Ner-like protein) gene was isolated from Escherichia coli. The nucleotide sequence of a 1,342-base-pair chromosomal DNA fragment containing the nlp gene was analyzed. It contained two open reading frames; one encoded 91 amino acid residues with an Mr of 10,361, and the other (ORFX) encoded 131 amino acid residues of the carboxyl-terminal region of a truncated polypeptide. The amino acid sequence deduced from the DNA sequence of nlp was highly homologous (62 to 63%) to the Ner proteins of bacteriophages Mu and D108. The amino-terminal region of Nlp deduced from the complete open reading frame contained a presumed DNA-binding region. The nlp gene was located at 69.3 min on the E. coli genetic map.

Dimer formation of octaprenyl-diphosphate synthase (IspB) is essential for chain length determination of ubiquinone.

Ubiquinone (Q), composed of a quinone core and an isoprenoid side chain, is a key component of the respiratory chain and is an important antioxidant. In Escherichia coli, the side chain of Q-8 is synthesized by octaprenyl-diphosphate synthase, which is encoded by an essential gene, ispB. To determine how IspB regulates the length of the isoprenoid, we constructed 15 ispB mutants and expressed them in E. coli and Saccharomyces cerevisiae. The Y38A and R321V mutants produced Q-6 and Q-7, and the Y38A/R321V double mutant produced Q-5 and Q-6, indicating that these residues are involved in the determination of chain length. E. coli cells (ispB::cat) harboring an Arg-321 mutant were temperature-sensitive for growth, which indicates that Arg-321 is important for thermostability of IspB. Intriguingly, E. coli cells harboring wild-type ispB and the A79Y mutant produced mainly Q-6, although the activity of the enzyme with the A79Y mutation was completely abolished. When a heterodimer of His-tagged wild-type IspB and glutathione S-transferase-tagged IspB(A79Y) was formed, the enzyme produced a shorter length isoprenoid. These results indicate that although the A79Y mutant is functionally inactive, it can regulate activity upon forming a heterodimer with wild-type IspB, and this dimer formation is important for the determination of the isoprenoid chain length.