Secondary literature sources for TPR
The following references were automatically generated.
- Ramagopal UA, Ramakumar S, Sahal D, Chauhan VS
- De novo design and characterization of an apolar helical hairpin peptide at atomic resolution: Compaction mediated by weak interactions.
- Proc Natl Acad Sci U S A. 2001; 98: 870-4
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Design of helical super secondary structural motifs is expected to provide important scaffolds to incorporate functional sites, thus allowing the engineering of novel miniproteins with function. An alpha,beta-dehydrophenylalanine containing 21-residue apolar peptide was designed to mimic the helical hairpin motif by using a simple geometrical design strategy. The synthetic peptide folds into the desired structure as assessed crystallographically at 1.0-A resolution. The two helices of the helical-hairpin motif, connected by a flexible (Gly)(4) linker, are docked to each other by the concerted influence of weak interactions. The folding of the peptide without binary patterning of amino acids, disulfide bonds, or metal ions is a remarkable observation. The results demonstrate that preferred interactions among the hydrophobic residues selectively discriminate their putative partners in space, leading to the unique folding of the peptide, also a hallmark of the unique folding of hydrophobic core in globular proteins. We demonstrate here the engineering of molecules by using weak interactions pointing to their possible further exploitation in the de novo design of protein super secondary structural elements.
- Zhang CT, Zhang R
- S curve, a graphic representation of protein secondary structure sequence and its applications.
- Biopolymers. 2000; 53: 539-49
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A secondary structure sequence is a symbolic string composed of three kinds of letters, indicating the helix, strand, and coil (including turns), respectively. A graphic representation for this abstract symbolic sequence is proposed here, called the S curve. The S curve is the unique representation for a given secondary structure sequence in the sense that the sequence and the S curve can be uniquely determined from the other. Therefore, the S curve contains all the information that the secondary structure sequence contains. Different geometrical properties of the S curve are studied in details, which reflect the basic characteristics of the secondary structure sequences. The S curves are used to display, analyze, and compare the secondary structure sequences. Detailed application examples are presented. One advantage of the S curve methodology is that the main patterns of a given secondary structure sequence can be grasped quickly in a perceivable form. This is particularly useful in the cases in which longer sequences are involved and structures of proteins are unknown.
- Zhang H, Grishin NV
- The alpha-subunit of protein prenyltransferases is a member of the tetratricopeptide repeat family.
- Protein Sci. 1999; 8: 1658-67
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Lipidation catalyzed by protein prenyltransferases is essential for the biological function of a number of eukaryotic proteins, many of which are involved in signal transduction and vesicular traffic regulation. Sequence similarity searches reveal that the alpha-subunit of protein prenyltransferases (PTalpha) is a member of the tetratricopeptide repeat (TPR) superfamily. This finding makes the three-dimensional structure of the rat protein farnesyltransferase the first structural model of a TPR protein interacting with its protein partner. Structural comparison of the two TPR domains in protein farnesyltransferase and protein phosphatase 5 indicates that variation in TPR consensus residues may affect protein binding specificity through altering the overall shape of the TPR superhelix. A general approach to evolutionary analysis of proteins with repetitive sequence motifs has been developed and applied to the protein prenyltransferases and other TPR proteins. The results suggest that all members in PTalpha family originated from a common multirepeat ancestor, while the common ancestor of PTalpha and other members of TPR superfamily is likely to be a single repeat protein.
- Breeden L
- Start-specific transcription in yeast.
- Curr Top Microbiol Immunol. 1996; 208: 95-127
- Mizuta K, Hashimoto T, Otaka E
- The evolutionary relationships between homologs of ribosomal YL8 protein and YL8-like proteins.
- Curr Genet. 1995; 28: 19-25
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We previously reported the sequence of YL8A, one of the two genes encoding yeast ribosomal protein YL8. With the aim of conducting an evolutionary study we have cloned and sequenced a second gene, YL8B. The disruption of both genes is lethal. Unlike other duplicated ribosomal protein genes, each open reading frame is interrupted by two introns containing long conserved sequences. A comparison of nucleotide and amino-acid sequences reveals that the duplication of the YL8 gene must have occurred very recently. Alignment and phylogenetic analysis of the amino-acid sequences of YL8-related proteins from various species show the existence not only of YL8 ribosomal proteins but also of a family of YL8-like proteins. These are present in at least three species of yeast and seem to be functionally distinct from ribosomal proteins.
- Hughes R, Chan FY, White RA, Zon LI
- Cloning and chromosomal localization of a mouse cDNA with homology to the Saccharomyces cerevisiae gene zuotin.
- Genomics. 1995; 29: 546-50
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The eukaryotic DnaJ homologs form a family of proteins with diverse functions. One member of the family, the Saccharomyces cerevisiae gene zuotin, was isolated for its ability to bind Z-DNA. Here, we have isolated a mouse cDNA called ZRF1 (for zuotin-related factor1) with significant homology to zuotin. The DnaJ domain and candidate phosphorylation sites of zuotin and ZRF1 are highly conserved. ZRF1 gene is localized on chromosome 5. The structural similarity of zuotin and ZRF1 suggests conservation of function of this DnaJ subfamily.
- Bidard F, Bony M, Blondin B, Dequin S, Barre P
- The Saccharomyces cerevisiae FLO1 flocculation gene encodes for a cell surface protein.
- Yeast. 1995; 11: 809-22
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The sequencing of a 6619 bp region encoding for a flocculation gene previously cloned from a strain defined as FLO5 (Bidard et al., 1994) has revealed that it was a FLO1 gene. The FLO1 gene product has been localized at the cell surface of the yeast cell by immunofluorescent microscopy. The Flo1 protein contains four regions with repeated sequences which account for about 70% of the amino acids of this protein. A functional analysis of the major repeated region has revealed that it plays an important role in determining the flocculation level. A gene disruption experiment has shown that FLO5 strain STX 347-1D contains at least two flocculation genes of the FLO1 type but that they are supposed to be inactive and do not contribute to its flocculation. However, enzyme-linked immunosorbent assays performed on intact cells have revealed that a protein expressed at the cell surface of the FLO5 strain STX 347-1D is antigenically related to Flo1p. A deletion analysis of the 5' region of the FLO1 gene has shown that the expression is submitted to controls which depend on the genetic background of the strain.
- Uemura H, Jigami Y
- A new essential gene GCR4 located in the upstream region of GCR1.
- Yeast. 1995; 11: 1093-101
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A new essential gene of Saccharomyces cerevisiae was found upstream of GCR1. Its cloning and sequencing predict a 280 amino acid protein (32,577 Da). The predicted protein is fairly hydrophobic, and a search of the database did not identify any homologous proteins. A LEU2 disruption at codon 104 was lethal, but disruption at codon 221 showed a temperature-sensitive conditional growth phenotype. Abnormalities were observed in some glycolytic enzyme levels.
- Lamb JR, Michaud WA, Sikorski RS, Hieter PA
- Cdc16p, Cdc23p and Cdc27p form a complex essential for mitosis.
- EMBO J. 1994; 13: 4321-8
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Cdc16p, Cdc23p and Cdc27p are all essential proteins required for cell cycle progression through mitosis in Saccharomyces cerevisiae. All three proteins contain multiple tandemly repeated 34 amino acid tetratricopeptide repeats (TPRs). Using two independent assays, two-hybrid analysis in vivo and co-immunoprecipitation in vitro, we demonstrate that Cdc16p, Cdc23p and Cdc27p self associate and interact with one another to form a macromolecular complex. A temperature sensitive mutation in the most highly conserved TPR domain of Cdc27p results in a greatly reduced ability to interact with Cdc23p, but has no effect on interactions with wild-type Cdc27p or Cdc16p. The specificity of this effect indicates that TPRs can mediate protein-protein interactions and that this mutation may define an essential interaction for cell cycle progression in yeast. The conservation of at least two of the three proteins from yeast to man suggests that this protein complex is essential for mitosis in a wide range of eukaryotes.
- Levin DE, Stevenson WD, Watanabe M
- Evidence against the existence of the purported Saccharomyces cerevisiae PKC2 gene.
- Curr Biol. 1994; 4: 990-5
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BACKGROUND: The existence of a Saccharomyces cerevisiae gene encoding a novel isoform of protein kinase C was reported recently in this journal. RESULTS: We demonstrate here that, firstly, the purported PKC2 gene does not reside at the chromosomal location to which it was assigned; secondly, it does not exist as a contiguous sequence in the S. cerevisiae genome; thirdly, some of its reported sequences do exist within other yeast genes; and fourthly, some of its reported sequences, encoding regions of the predicted protein related to protein kinase C, do not exist in any context in the yeast genome. CONCLUSIONS: We conclude from these studies that the PKC2 gene is a composite construction of unrelated yeast and non-yeast sequences.
- Matsumoto Y, Sarkar G, Sommer SS, Wickner RB
- A yeast antiviral protein, SKI8, shares a repeated amino acid sequence pattern with beta-subunits of G proteins and several other proteins.
- Yeast. 1993; 9: 43-51
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SKI8 is a yeast antiviral gene, essential for controlling the propagation of M double-stranded RNA (dsRNA) and thus for preventing virus-induced cytopathology. Our DNA sequence of SKI8 shows that it encodes a 397 amino acid protein containing two copies of a 31 amino acid repeat pattern first identified in mammalian beta-transducin and Cdc4p of yeast. There are also four copies of this repeat in yeast Mak11p, necessary for M dsRNA propagation, and three copies in the putative product of the Dictyostelium AAC3 gene. Analysis of 36 cases of the repeat unit shows they have a consensus predicted structure: N-helix-sheet-turn-sheet-turn-sheet-helix-C.
- de Winde JH, Grivell LA
- Global regulation of mitochondrial biogenesis in Saccharomyces cerevisiae.
- Prog Nucleic Acid Res Mol Biol. 1993; 46: 51-91
- Brigati C, Kurtz S, Balderes D, Vidali G, Shore D
- An essential yeast gene encoding a TTAGGG repeat-binding protein.
- Mol Cell Biol. 1993; 13: 1306-14
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A yeast gene encoding a DNA-binding protein that recognizes the telomeric repeat sequence TTAGGG found in multicellular eukaryotes was identified by screening a lambda gt11 expression library with a radiolabeled TTAGGG multimer. This gene, which we refer to as TBF1 (TTAGGG repeat-binding factor 1), encodes a polypeptide with a predicted molecular mass of 63 kDa. The TBF1 protein, produced in vitro by transcription and translation of the cloned gene, binds to (TTAGGG)n probes and to a yeast telomeric junction sequence that contains two copies of the sequence TTAGGG separated by 5 bp. TBF1 appears to be identical to a previously described yeast TTAGGG-repeat binding activity called TBF alpha. TBF1 produced in vitro yields protein-DNA complexes with (TTAGGG)n probes that have mobilities on native polyacrylamide gels identical to those produced by partially purified TBF alpha from yeast cells. Furthermore, when extracts are prepared from a strain containing a TBF1 gene with an antigen tag, we find that the antigen copurifies with the predominant (TTAGGG)n-binding activity in the extracts. The DNA sequence of TBF1 was determined. The predicted protein sequence suggests that TBF1 may contain a nucleotide-binding domain, but no significant similarities to any other known proteins were identified, nor was an obvious DNA-binding motif apparent. Diploid cells heterozygous for a tbf1::URA3 insertion mutation are viable but upon sporulation give rise to tetrads with only two viable spores, both of which are Ura-, indicating that the TBF1 gene is essential for growth. Possible functions of TBF1 (TFB alpha) are discussed in light of these new results.
- Boguski MS, Murray AW, Powers S
- Novel repetitive sequence motifs in the alpha and beta subunits of prenyl-protein transferases and homology of the alpha subunit to the MAD2 gene product of yeast.
- New Biol. 1992; 4: 408-11
- Stankis MM, Specht CA, Yang H, Giasson L, Ullrich RC, Novotny CP
- The A alpha mating locus of Schizophyllum commune encodes two dissimilar multiallelic homeodomain proteins.
- Proc Natl Acad Sci U S A. 1992; 89: 7169-73
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The A alpha mating locus is one of four multiallelic loci that govern sexual development in the basidiomycete fungus Schizophyllum commune. We have determined the nucleotide sequence encoding three A alpha mating types, A alpha 1, A alpha 3, and A alpha 4. We have found that the locus for A alpha 3 and A alpha 4 consists of two genes: Y and Z. The locus for A alpha 1 encodes only one gene, Y. The Z polypeptides encoded by different alleles exhibit 42% identity. The Y polypeptides exhibit 49-54% identity. The finding that the deduced Z and Y polypeptides have homeodomain motifs suggests that these polypeptides may be DNA-binding regulatory proteins that control the expression of developmental genes. The deduced Z polypeptide also has acidic regions that might be functionally analogous to the acidic regions in yeast GAL4 and GCN4 that activate transcription. The Y polypeptide has a serine-rich region and a basic region that shows some identity to the lysine-rich region of H1 histones.
- van der Voorn L, Ploegh HL
- The WD-40 repeat.
- FEBS Lett. 1992; 307: 131-4
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An amino acid sequence motif, called the WD-40 repeat, has been found as a repeat in a large variety of proteins that do not share any obvious functional properties. At present, the function of the repeated motif is not known for any of these proteins. Interestingly, recent experiments in yeast indicate that several proteins containing the WD-40 repeat are genetically associated with members of the TPR-family, a protein family that is characterized by the presence of another repeated motif of unknown function: the tetratricopeptide repeat. It is conceivable that proteins containing the WD-40 repeat interact physically with members of the TPR-family via their respective repeated motifs.
- Ekwall K, Kermorgant M, Dujardin G, Groudinsky O, Slonimski PP
- The NAM8 gene in Saccharomyces cerevisiae encodes a protein with putative RNA binding motifs and acts as a suppressor of mitochondrial splicing deficiencies when overexpressed.
- Mol Gen Genet. 1992; 233: 136-44
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We have characterized the nuclear gene NAM8 in Saccharomyces cerevisiae. It acts as a suppressor of mitochondrial splicing deficiencies when present on a multicopy plasmid. The suppressed mutations affect RNA folding and are located in both group I and group II introns. The gene is weakly transcribed in wild-type strains, its overexpression is a prerequisite for the suppressor action. Inactivation of the NAM8 gene does not affect cell viability, mitochondrial function or mitochondrial genome stability. The NAM8 gene encodes a protein of 523 amino acids which includes two conserved (RNP) motifs common to RNA-binding proteins from widely different organisms. This homology with RNA-binding proteins, together with the intronic location of the suppressed mitochondrial mutations, suggests that the NAM8 protein could be a non-essential component of the mitochondrial splicing machinery and, when present in increased amounts, it could convert a deficient intron RNA folding pattern into a productive one.
- Schmidt C et al.
- Complete cDNA sequence of chicken vigilin, a novel protein with amplified and evolutionary conserved domains.
- Eur J Biochem. 1992; 206: 625-34
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The complete cDNA (4375 bp), coding for a new protein called vigilin, was isolated from chicken chondrocytes. The cDNA shows an open reading frame of 1270 amino acids which are organized in 14 tandemly repeated homologous domains. Each domain consists of two subdomains, one with a conserved sequence motif of 35 amino acids (subdomain A) and another one with a presumptive alpha-helical structure of 21-33 amino acids (subdomain B). 149 amino acids at the N-terminus and 71 amino acids at the C-terminus of vigilin do not show the characteristic domain structure. No sequence characteristic of a signal peptide has been found, which argues for an intracellular localisation of vigilin. Vigilin is highly expressed in freshly isolated chicken chondrocytes but little in chondrocytes after prolonged time in culture. Vigilin mRNA exists in two size species, 4.4 kb and 6.5 kb in length due to the usage of different polyadenylation sites. Comparison of the vigilin sequence with data bases showed a remarkable similarity to protein HX from Saccharomyces cerevisiae [Delahodde, A., Becam, A. M., Perea, J. & Jacq, C. (1986) Nucleic Acids Res. 14, 9213-9214]. The yeast protein consists of eight homologous domains with 11 conserved amino acid residues within a set of 35 amino acids. The N-terminal and C-terminal regions of vigilin and protein HX do not reveal any sequence similarity. These results, together with the demonstration of the characteristic vigilin sequence motif in a human cDNA clone, suggest that the repeats represent evolutionary conserved autonomous domains within a family of proteins found in yeast, chicken and man.
- Feuchter AE, Freeman JD, Mager DL
- Strategy for detecting cellular transcripts promoted by human endogenous long terminal repeats: identification of a novel gene (CDC4L) with homology to yeast CDC4.
- Genomics. 1992; 13: 1237-46
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Several families of repetitive sequences related to integrated retroviruses have been identified in the human genome. The largest of these families, the RTVL-H family, has close to 1000 members in addition to a similar number of solitary long terminal repeats (LTRs) dispersed on all chromosomes. Previous work has shown that the expression of genomic RTVL-H elements is driven by their LTRs and that some LTRs can promote expression of a reporter gene. These observations suggest that some endogenous RTVL-HLTRs may naturally regulate the transcription of adjacent cellular genes or that rearrangements involving these elements may cause aberrant gene expression. To investigate this possibility, we have used a differential screening strategy to identify chimeric cDNA clones derived from LTR-promoted transcripts. Here we report the identification and analysis of four such clones isolated from an NTera2D1 (teratocarcinoma) cDNA library. Two of the clones, AF-1 and AF-2, contain termination codons in all reading frames. Another clone, AF-4, contains LTR sequences linked in the genome to a CpG island. The fourth clone, AF-3, contains an 862-bp open reading frame representing part of a novel gene (CDC4L) with homology to the yeast cell division cycle gene CDC4. These findings indicate that RTVL-H elements may be involved in the regulation of diverse cellular transcripts in human cells.
- Schneider R, Schweiger M
- The yeast RNA1 protein, necessary for RNA processing, is homologous to the human ribonuclease/angiogenin inhibitor (RAI).
- Mol Gen Genet. 1992; 233: 315-8
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Mutations in the RNA1 gene of Saccharomyces cerevisiae, which encodes an essential cytosolic protein, affect the production and processing of all major classes of RNA. The mechanisms underlying these effects are not at all understood. Detailed comparative sequence analyses revealed that the RNA1 protein belongs to a superfamily, the members of which contain repetitive "leucine-rich motifs" (LRM). Within this superfamily RNA1 is most closely related to the ribonuclease/angiogenin inhibitor (RAI), which is a tightly binding inhibitor of ribonucleolytic activities in mammals. These results not only provide important clues to the structure, function and evolution of the RNA1 protein, but also have intriguing implications for possible novel functions of RAI.
- Starr CM, Hanover JA
- A common structural motif in nuclear pore proteins (nucleoporins)
- Bioessays. 1991; 13: 145-6
- Phillips CL, Vershon AK, Johnson AD, Dahlquist FW
- Secondary structure of the homeo domain of yeast alpha 2 repressor determined by NMR spectroscopy.
- Genes Dev. 1991; 5: 764-72
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The yeast alpha 2 protein is a regulator of cell type in Saccharomyces cerevisiae. It represses transcription of a set of target genes by binding to an operator located upstream of each of these genes. The alpha 2 protein shares weak sequence similarity with members of the homeo domain family; the homeo domain is a 60-amino-acid segment found in many eukaryotic transcriptional regulators. In this paper we address the question of whether alpha 2 is structurally related to prototypical members of the homeo domain family. We used solution 1H and 15N nuclear magnetic resonance [NMR] spectroscopy to determine the secondary structure of an 83-amino-acid residue fragment of alpha 2 that contains the homeo domain homology. We have obtained resonance assignments for the backbone protons and nitrogens of the entire 60-residue region of the putative homeo domain and for most of the remainder of the alpha 2 fragment. The secondary structure was determined by using NOE connectivities between backbone protons, 3JHN-H alpha coupling constants, and dynamical information from the hydrogen exchange kinetics of the backbone amides. Three helical segments exist in the alpha 2 fragment consisting of residues 11-23, 32-42, and 46-60 (corresponding to residues 138-150, 159-169, and 173-187 of the intact protein). The positions of these three helices correspond extremely well to those of the Drosophila Antennapedia (Antp) and engrailed (en) homeo domains, whose three-dimensional structures have recently been determined by NMR spectroscopy and X-ray crystallography, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)
- Roof DM, Meluh PB, Rose MD
- Multiple kinesin-related proteins in yeast mitosis.
- Cold Spring Harb Symp Quant Biol. 1991; 56: 693-703
- Carbone ML, Solinas M, Sora S, Panzeri L
- A gene tightly linked to CEN6 is important for growth of Saccharomyces cerevisiae.
- Curr Genet. 1991; 19: 1-8
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Transcriptional analysis of the region flanking the left boundary of the centromere of chromosome VI revealed the presence of a gene immediately adjacent to CEN6. The transcription of the gene is directed toward the centromere, and nucleotide sequence analysis showed that the coding region terminates only 50 bp away from CEN6. Our results extend to chromosome VI the observation that centromere-flanking regions of S. cerevisiae are transcriptionally active. Disruption of the coding region of the gene showed that its product, whilst not essential for cell viability, is important for normal cell growth. The gene has been termed DEG1 (DEpressed Growth rate). Comparison of the deduced amino acid sequence of DEG1 with a protein sequence databank revealed homology with the enzyme tRNA pseudouridine synthase I of E. coli.
- Kearsey S
- The SFL2 (TUP1?) protein of Saccharomyces cerevisiae contains a repeating motif homologous to beta subunits of G proteins.
- Gene. 1991; 98: 147-8
- Kormanec J, Schaaff-Gerstenschlager I, Zimmermann FK, Perecko D, Kuntzel H
- Nuclear migration in Saccharomyces cerevisiae is controlled by the highly repetitive 313 kDa NUM1 protein.
- Mol Gen Genet. 1991; 230: 277-87
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We have isolated a novel gene (NUM1) with unusual internal periodicity. The NUM1 gene encodes a 313 kDa protein with a potential Ca2+ binding site and a central domain containing 12 almost identical tandem repeats of a 64 amino acid polypeptide. num1-disrupted strains grow normally, but contain many budded cells with two nuclei in the mother cell instead of a single nucleus at the bud neck, while all unbudded cells are uninucleate. This indicates that most G2 nuclei divide in the mother before migrating to the neck, followed by the migration of one of the two daughter nuclei into the bud. Furthermore, haploid num1 strains tend to diploidize during mitosis, and homozygous num1 diploid or tetraploid cells sporulate to form many budded asci with up to eight haploid or diploid spores, respectively, indicating that meiosis starts before nuclear redistribution and cytokinesis. Our data suggest that the NUM1 protein is involved in the interaction of the G2 nucleus with the bud neck.
- Swanson MS, Malone EA, Winston F
- SPT5, an essential gene important for normal transcription in Saccharomyces cerevisiae, encodes an acidic nuclear protein with a carboxy-terminal repeat.
- Mol Cell Biol. 1991; 11: 4286-4286
- Mellor J et al.
- CPF1, a yeast protein which functions in centromeres and promoters.
- EMBO J. 1990; 9: 4017-26
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Centromeres and several promoters of Saccharomyces cerevisiae contain a highly conserved octanucleotide, RTCACRTG, called CDEI. Using biochemical, genetic and structural analyses, we show that the same protein binds in vivo to CDEI sites in centromeres and in promoters. This protein, called CPF1 for centromere promoter factor, binds DNA as a dimer. Inactivation of the gene is not lethal but leads to a partial loss of the centromere function and to a Met- phenotype. Changes of the chromatin structure due to inactivation of CPF1 are seen at centromeres and at several CDEI-carrying promoters (e.g. MET25, TRP1, GAL2). However promoter activities are affected in diverse ways making it presently difficult to describe a function for CPF1 in gene expression. The sequence of the cloned gene reveals in the carboxy-terminal part two potential amphipathic helices preceded by a positively charged stretch of amino acids very similar to the helix-loop-helix domains recently identified in factors controlling tissue specific transcription in higher eukaryotes. Carboxy-terminal truncations of CPF1 lacking this domain no longer bind to CDEI. The amino-terminal half of CPF1 carries two clusters of negatively charged amino acid residues. Surprisingly, deletions of these clusters still render cells Met+ and lead only to a marginal decrease in centromere activity.
- Cai M, Davis RW
- Yeast centromere binding protein CBF1, of the helix-loop-helix protein family, is required for chromosome stability and methionine prototrophy.
- Cell. 1990; 61: 437-46
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The centromere and its binding proteins constitute the kinetochore structure of metaphase chromosomes, which is crucial for the high accuracy of the chromosome segregation process. Isolation and analysis of the gene encoding a centromere binding protein from the yeast S. cerevisiae, CBF1, are described in this paper. DNA sequence analysis of the CBF1 gene reveals homology with the transforming protein myc and a family of regulatory proteins known as the helix-loop-helix (HLH) proteins. Disruption of the CBF1 gene caused a decrease in the growth rate, an increase in the rate of chromosome loss/nondisjunction, and hypersensitivity to the antimitotic drug thiabendazole. Unexpectedly, the cbf1 null mutation concomitantly resulted in a methionine auxotrophic phenotype, which suggests that CBF1, like other HLH proteins in higher eukaryotic cells, participates in the regulation of gene expression.
- Legrain P, Choulika A
- The molecular characterization of PRP6 and PRP9 yeast genes reveals a new cysteine/histidine motif common to several splicing factors.
- EMBO J. 1990; 9: 2775-81
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prp6 and prp9 thermosensitive (ts) mutants are affected in pre-mRNA splicing and transport from the nucleus to the cytoplasm. PRP6 and PRP9 wild-type alleles have been sequenced. DNA sequence analysis reveals homologies in the 5' and 3' non-coding regions, suggesting a common regulation of gene expression. PRP6 and PRP9 genes encode a 899 amino acid and a 530 amino acid protein, respectively. The PRP6 protein has repeated motifs that evoke helix-loop-helix structures. Both PRP6 and PRP9 proteins have cysteine/histidine motifs loosely related to those found in zinc finger proteins. The substitution of some, but not all, of these residues by directed mutagenesis has a critical effect on the protein function. Homology searches reveal that two other proteins known to be involved in the nuclear splicing pathway--the yeast PRP11 and the human U1C proteins--contain similar sequences. The five cysteine/histidine motifs found in these four proteins display amino acid similarities in addition to the cysteine and histidine residues, indicating that they participate in biological structures or functions related to the splicing process. In addition, PRP6 and PRP9 exhibit leucine repeat motifs which may be implicated in protein interactions. The prp6 and prp9 ts mutations have been mapped and sequenced.
- Aas SF, Rognes SE
- Nucleotide sequence of the yeast THR4 gene encoding threonine synthase.
- Nucleic Acids Res. 1990; 18: 665-665
- Berben G, Legrain M, Gilliquet V, Hilger F
- The yeast regulatory gene PHO4 encodes a helix-loop-helix motif.
- Yeast. 1990; 6: 451-4
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Evidence is presented, based on sequence comparisons and secondary structure prediction, of the presence of a DNA-binding and dimerization helix-loop-helix motif in the yeast transcription activator PHO4. Interest in the existence of this first known motif in yeast is discussed.
- Hadwiger JA, Reed SI
- Nucleotide sequence of the Saccharomyces cerevisiae CLN1 and CLN2 genes.
- Nucleic Acids Res. 1990; 18: 4025-4025
- Suzuki K, Hashimoto T, Otaka E
- Yeast ribosomal proteins: XI. Molecular analysis of two genes encoding YL41, an extremely small and basic ribosomal protein, from Saccharomyces cerevisiae.
- Curr Genet. 1990; 17: 185-90
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Two genes encoding ribosomal protein YL41 were cloned from Saccharomyces cerevisiae chromosomal DNA. Both genes contain an uninterrupted region of only 75 nucleotides coding for a protein of 3.3 kD. Within the coding regions the nucleotide sequences are virtually identical, whereas in both the 5'- and 3'-flanking regions the two genes differ significantly from each other. The deduced protein shows an arginine and lysine content of 68 percent, i.e., 17 out of 25 residues, and the basic residues are evenly distributed over the molecule. When compared to the ribosomal protein sequences currently available no counterpart to YL41 could be found in prokaryotes and it seems likely that YL41 is a eukaryote-specific ribosomal protein.
- Asher EB, Groudinsky O, Dujardin G, Altamura N, Kermorgant M, Slonimski PP
- Novel class of nuclear genes involved in both mRNA splicing and protein synthesis in Saccharomyces cerevisiae mitochondria.
- Mol Gen Genet. 1989; 215: 517-28
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We have cloned three distinct nuclear genes, NAM1, NAM7, and NAM8, which alleviate mitochondrial intron mutations of the cytochrome b and COXI (subunit I of cytochrome oxidase) genes when present on multicopy plasmids. These nuclear genes show no sequence homology to each other and are localized on different chromosomes: NAM1 on chromosome IV, NAM7 on chromosome XIII and NAM8 on chromosome VIII. Sequence analysis of the NAM1 gene shows that it encodes a protein of 440 amino acids with a typical presequence that would target the protein to the mitochondrial matrix. Inactivation of the NAM1 gene by gene transplacement leads to a dramatic reduction of the overall synthesis of mitochondrial protein, and a complete absence of the COXI protein which is the result of a specific block in COXI pre-mRNA splicing. The possible mechanisms by which the NAM1 gene product may function are discussed.
- Diffley JF, Stillman B
- Similarity between the transcriptional silencer binding proteins ABF1 and RAP1.
- Science. 1989; 246: 1034-8
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The yeast ARS binding factor 1 (ABF1)--where ARS is an autonomously replicating sequence--and repressor/activator protein 1 (RAP1) have been implicated in DNA replication, transcriptional activation, and transcriptional silencing. The ABF1 gene was cloned and sequenced and shown to be essential for viability. The predicted amino acid sequence contains a novel sequence motif related to the zinc finger, and the ABF1 protein requires zinc and unmodified cysteine residues for sequence-specific DNA binding. Interestingly, ABF1 is extensively related to its counterpart, RAP1, and both proteins share a region of similarity with SAN1, a suppressor of certain SIR4 mutations, suggesting that this region may be involved in mediating SIR function at the silent mating type loci.
- Komar AA, Iurkevich VV
- [Partial homology of the sequences of structural genes for yeast secretory and membrane proteins; identification of probable sorting-transport sites of these proteins]
- Dokl Akad Nauk SSSR. 1988; 299: 498-502
- Toda T, Sass P
- The cAMP-dependent protein kinase genes in yeast.
- Oxf Surv Eukaryot Genes. 1988; 5: 133-61
- Sarid J, Leder P
- Sequence analysis of a yeast genomic DNA fragment sharing homology with the human c-myc gene.
- Nucleic Acids Res. 1988; 16: 4725-4725
- Surguchev AP, Sudarikov AB
- [Analysis of the primary structure of gene sup1 and its protein product in connection with the possible evolutionary origin of the gene]
- Dokl Akad Nauk SSSR. 1987; 296: 238-42
- Laughon A, Gesteland RF
- Primary structure of the Saccharomyces cerevisiae GAL4 gene.
- Mol Cell Biol. 1984; 4: 260-7
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The GAL4 gene encodes a positive regulator of the galactose-inducible genes in Saccharomyces cerevisiae. Recently, GAL4 has been cloned and its 2.8-kilobase mRNA has been identified. We report here the DNA sequence of GAL4 and the mapping of the 5' and 3' ends of its transcripts. The region sequenced contains a single open reading frame, 881 codons long, which could encode a 99,350-dalton protein. The 5' ends of the GAL4 transcripts fall into two clusters. Transcripts which begin at the upstream cluster would encode the 99,350-dalton protein, whereas those starting at the downstream cluster may result in the synthesis of a shorter, 91,600-dalton protein. The putative GAL4 proteins contain an amino acid sequence near their amino termini which resembles a DNA-binding motif found in bacterial and phage repressors and gene activator proteins.
