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Hochstoeger T, Chao JA. Towards a molecular understanding of the 5'TOP motif in regulating translation of ribosomal mRNAs. Semin Cell Dev Biol 2024; 154:99-104. [PMID: 37316417 DOI: 10.1016/j.semcdb.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 04/14/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023]
Abstract
Vertebrate cells have evolved a simple, yet elegant, mechanism for coordinated regulation of ribosome biogenesis mediated by the 5' terminal oligopyrimidine motif (5'TOP). This motif allows cells to rapidly adapt to changes in the environment by specifically modulating translation rate of mRNAs encoding the translation machinery. Here, we provide an overview of the origin of this motif, its characterization, and progress in identifying the key regulatory factors involved. We highlight challenges in the field of 5'TOP research, and discuss future approaches that we think will be able to resolve outstanding questions.
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Affiliation(s)
- Tobias Hochstoeger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
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2
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Jang TH, Park JH, Jeon JH, Lee DS, Choi K, Kim IG, Kim YW, Park HH. Crystallization and preliminary X-ray crystallographic studies of the N-terminal domain of human ribosomal protein L7a (RPL7a). Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:510-2. [PMID: 21505254 PMCID: PMC3080163 DOI: 10.1107/s1744309111006415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 02/20/2011] [Indexed: 11/10/2022]
Abstract
Ribosomal proteins are a major component of ribosomes, which catalyze protein synthesis. One ribosomal protein, L7a (RPL7a), which is a component of the 60S large ribosomal subunit, has additional functions involved in cell growth and differentiation that occur via interaction with human thyroid hormone receptor (THR) and retinoic acid receptor (RAR) and in turn inhibit the activities of the two nuclear hormone receptors. In this study, the N-terminal domain of human RPL7a was overexpressed in Escherichia coli using an engineered C-terminal His tag. The N-terminal domain of human RPL7a was then purified to homogeneity and crystallized at 293 K. X-ray diffraction data were collected to a resolution of 3.5 Å from a crystal belonging to the tetragonal space group P4(1)22 or P4(3)22 with unit-cell parameters a = 92.28, b = 92.28, c = 236.59 Å.
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Affiliation(s)
- Tae-ho Jang
- Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
| | - Jin Hee Park
- Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
| | - Ju-Hong Jeon
- Department of Physiology and Institute of Dermatological Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong-Sup Lee
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kihang Choi
- Department of Chemistry, Korea University, Seoul, Republic of Korea
| | - In-Gyu Kim
- Department of Biochemistry and Molecular Biology/Aging and Apoptosis Research Center (AARC), Seoul National University College of Medicine, Seoul Republic of Korea
| | - Young Whan Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine and Lung Institute of Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyun Ho Park
- Graduate School of Biochemistry, Yeungnam University, Gyeongsan, Republic of Korea
- School of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
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3
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Armes N, Gilley J, Fried M. The comparative genomic structure and sequence of the surfeit gene homologs in the puffer fish Fugu rubripes and their association with CpG-rich islands. Genome Res 1997; 7:1138-52. [PMID: 9414319 DOI: 10.1101/gr.7.12.1138] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The puffer fish Fugu rubripes (Fugu) has a compact genome approximately one-seventh the size of man, mainly owing to small intron size and the presence of few dispersed repetitive DNA elements, which greatly facilitates the study of its genes at the genomic level. It has been shown previously that, whereas the Surfeit genes are tightly clustered at a single locus in mammals and birds, the genes are found at three separate loci in the Fugu genome. Here, Fugu gene homologs of all six Surfeit genes (Surf-1 to Surf-6) have been cloned and sequenced, and their gene structure has been compared with that of their mammalian and avian homologs. The predicted protein products of each gene are well conserved between vertebrate species, and in most cases their gene structures are identical to their mammalian and avian homologs except for the Fugu Surf-6 gene, which was found to lack an intron present in the mouse gene. In addition, we have identified conserved regulatory elements at the 5' and 3' ends of the Surf-3/rpL7a gene by comparison with the mammalian and chicken Surf-3/rpL7a gene homologs, including the presence of a polypyrimidine tract at the extreme 5' end of this ribosomal protein gene. The Fugu Surfeit gene homologs appear to be associated with CpG-rich islands, like the Surfeit genes in higher vertebrates, but these Fugu CpG islands are similar to the nonclassical islands characteristic of other fish species. Our observations support the use of the Fugu genome to study vertebrate gene structure, to predict the structure of mammalian genes, and to identify vertebrate regulatory elements. [The sequence data described in this paper have been submitted to the data library under accession nos. Y15170 (Surf-2, Surf-4), Y15171 (Surf-3, Surf-1, Surf-6), and Y15172 (Surf-5.)]
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Affiliation(s)
- N Armes
- Eukaryotic Gene Organisation and Expression Laboratory, Imperial Cancer Research Fund, Lincoln's Inn Fields, London WC2A 3PX, UK
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4
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Clausse N, Jackers P, Jarès P, Joris B, Sobel ME, Castronovo V. Identification of the active gene coding for the metastasis-associated 37LRP/p40 multifunctional protein. DNA Cell Biol 1996; 15:1009-23. [PMID: 8985115 DOI: 10.1089/dna.1996.15.1009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A 37LRP/p40 polypeptide is of major interest because it is consistently up-regulated in cancer cells in correlation with their invasive and metastatic phenotype. Furthermore, this polypeptide presents intriguing multifunctional properties because it has been characterized as the precursor of the metastasis-associated 67-kD laminin receptor (67LR) and as a cytoplasmic ribosomal-associated protein. The isolation of the 37LRP/p40 gene is a prerequisite for identifying the molecular mechanisms responsible for the constant up-regulation of the 67LR expression in cancer cells. To date, the active 37LRP/p40 gene has never been identified in any species due to the existence of multiple pseudogenes in most vertebrates genomes. In this study, we report for the first time the gene structure and potential regulatory sequences of the 37 LRP/p40 gene. The chicken genome was selected to undergo this characterization because it is the only known vertebrate that bears a single 37 LRP/p40 gene copy. The 37 LRP/p40 active gene is composed of 7 exons and 6 introns and bears features characteristic of a ribosomal protein gene. It does not bear a classical TATA box and it exhibits several transcription initiation sites as demonstrated by RNase protection assay and primer extension. Analysis of potential regulatory regions suggests that gene expression is driven not only by the 5' genomic region but also by the 5' untranslated and intron 1 sequences. On the basis of gene structure and extensive protein evolutionary study, we found that the carboxyterminal domain of the protein is a conserved lock-and-key structure/function domain that could be involved in the biosynthesis of the higher-molecular-weight 67-kD laminin receptor in vertebrates, whereas the central core of the protein would be responsible for the ribosome associated function. The first identification of the active 37LRP/p40 gene presented in this study is a critical step toward the isolation of the corresponding human gene and the understanding of the molecular mechanisms involved in the up-regulation of its expression during tumor invasion and metastasis.
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Affiliation(s)
- N Clausse
- Metastasis Research Laboratory, University of Liège, Belgium
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5
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Magoulas C, Fried M. The Surf-6 gene of the mouse surfeit locus encodes a novel nucleolar protein. DNA Cell Biol 1996; 15:305-16. [PMID: 8639267 DOI: 10.1089/dna.1996.15.305] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The Surfeit locus contains the tightest cluster of mammalian genes so far described. The five Surfeit genes (Surf-1 to -5) that have been previously isolated and characterized do not share any DNA or amino acid sequence homology. These Surfeit genes appear to be housekeeping genes, with the Surf-3 gene encoding the 1.7a ribosomal protein and the Surf-4 gene encoding an integral membrane protein most likely associated with the endoplasmic reticulum. In this work, we have isolated the Surf-6 gene, a sixth member of the Surfeit locus. The Surf-6 gene contains four exons spanning a genomic region of 14 kb and specifies a mRNA of 2,571 bases. Surf-6 has features common to housekeeping genes because its transcript is present in every tissue tested, its 5' end is associated with a CpG-rich island, and its promoter does not contain a canonical TATA box. The Surf-6 long open reading frame encodes a novel highly basic polypeptide of 355 amino acids (28% Arg and Lys). By immunofluorescence and immunoblot analyses, the Surf-6 protein has been found to be located in the nucleolus and by immunocytochemical microscopy to be localized predominantly in the nucleolar granular component, a structure that is involved in ribosome maturation. These results indicate that the novel Surf-6 gene is involved in a nucleolar function.
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Affiliation(s)
- C Magoulas
- Eukaryotic Gene Organisation and Expression Laboratory, Imperial Cancer Research Fund, Lincoln's Inn Fields, London, UK
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6
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Davies B, Fried M. The L19 ribosomal protein gene (RPL19): gene organization, chromosomal mapping, and novel promoter region. Genomics 1995; 25:372-80. [PMID: 7789970 DOI: 10.1016/0888-7543(95)80036-l] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The intron-containing genes encoding rat and human ribosomal protein L19 (RPL19) have been cloned. The DNA sequences of the entire rat RPL19 gene and the 5' end of the human RPL19 gene have been determined. Sequence comparison of corresponding regions of the two genes reveals a striking interspecies homology in the 5' upstream region, outside the transcribed and coding regions. The transcriptional start sites of the two genes have been determined and are identical. Both rat and human RPL19 genes have 5' ends associated with CpG islands. A promoter deletion analysis of the rat RPL19 gene suggests that this promoter may differ from those of all previously characterized ribosomal protein genes in requiring far upstream sequences for efficient gene expression. By fluorescence in situ hybridization analysis, the position of the human RPL19 gene has been sublocalized to 17q11 and may be coamplified with the erbB-2 gene in human breast cancer cells. The similarities and differences between RPL19 and other previously characterized ribosomal protein genes are discussed.
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Affiliation(s)
- B Davies
- Department of Eukaryotic Gene Organisation and Expression, Imperial Cancer Research Fund, London, United Kingdom
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7
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Structure and function of ribosomal protein S4 genes on the human and mouse sex chromosomes. Mol Cell Biol 1994. [PMID: 8139551 DOI: 10.1128/mcb.14.4.2485] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human sex-linked genes RPS4X and RPS4Y encode distinct isoforms of ribosomal protein S4. Insufficient expression of S4 may play a role in the development of Turner syndrome, the complex human phenotype associated with monosomy X. In mice, the S4 protein is encoded by an X-linked gene, Rps4, and is identical to human S4X; there is no mouse Y homolog. We report here the organization of the human RPS4X and RPS4Y and mouse Rps4 genes. Each gene comprises seven exons; the positions of introns are conserved. The 5' flanking sequences of human RPS4X and mouse Rps4 are very similar, while RPS4Y diverges shortly upstream of the transcription start site. In chickens, S4 is encoded by a single gene that is not sex linked. The chicken protein differs from human S4X by four amino acid substitutions, all within a region encoded by a single exon. Three of the four substitutions are also present in human S4Y, suggesting that the chicken S4 gene may have arisen by recombination between S4X- and S4Y-like sequences. Using isoform-specific antisera, we determined that human S4X and S4Y are both present in translationally active ribosomes. S4Y is about 10 to 15% as abundant as S4X in ribosomes from normal male placental tissue and 46,XY cultured cells. In 49,XYYYY cells, S4Y is about half as abundant as S4X. In 49,XXXXY cells, S4Y is barely detectable. These results bear on the hypothesized role of S4 deficiency in Turner syndrome.
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8
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Zinn AR, Alagappan RK, Brown LG, Wool I, Page DC. Structure and function of ribosomal protein S4 genes on the human and mouse sex chromosomes. Mol Cell Biol 1994; 14:2485-92. [PMID: 8139551 PMCID: PMC358616 DOI: 10.1128/mcb.14.4.2485-2492.1994] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The human sex-linked genes RPS4X and RPS4Y encode distinct isoforms of ribosomal protein S4. Insufficient expression of S4 may play a role in the development of Turner syndrome, the complex human phenotype associated with monosomy X. In mice, the S4 protein is encoded by an X-linked gene, Rps4, and is identical to human S4X; there is no mouse Y homolog. We report here the organization of the human RPS4X and RPS4Y and mouse Rps4 genes. Each gene comprises seven exons; the positions of introns are conserved. The 5' flanking sequences of human RPS4X and mouse Rps4 are very similar, while RPS4Y diverges shortly upstream of the transcription start site. In chickens, S4 is encoded by a single gene that is not sex linked. The chicken protein differs from human S4X by four amino acid substitutions, all within a region encoded by a single exon. Three of the four substitutions are also present in human S4Y, suggesting that the chicken S4 gene may have arisen by recombination between S4X- and S4Y-like sequences. Using isoform-specific antisera, we determined that human S4X and S4Y are both present in translationally active ribosomes. S4Y is about 10 to 15% as abundant as S4X in ribosomes from normal male placental tissue and 46,XY cultured cells. In 49,XYYYY cells, S4Y is about half as abundant as S4X. In 49,XXXXY cells, S4Y is barely detectable. These results bear on the hypothesized role of S4 deficiency in Turner syndrome.
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Affiliation(s)
- A R Zinn
- Howard Hughes Research Laboratories, Whitehead Institute, Cambridge, Massachusetts 02142
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9
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Chung S, Perry RP. The importance of downstream delta-factor binding elements for the activity of the rpL32 promoter. Nucleic Acids Res 1993; 21:3301-8. [PMID: 8341605 PMCID: PMC309771 DOI: 10.1093/nar/21.14.3301] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A salient feature of mammalian ribosomal protein genes is the location of promoter elements downstream, as well as upstream, of the transcriptional start point. Previous functional studies of the mouse rpL32 gene (Chung and Perry, Mol. Cell. Biol. 9, 2075; 1989) indicated that the first intron of this gene contains such an element. We show here that this element encompasses a binding site for a zinc finger nuclear protein known as delta (YY-1, muE1, UCRBP). The intronic delta site (delta i) is located 32 bp downstream of another delta site in the first exon (delta e). Transfection experiments with genes containing deleterious mutations in one or both delta sites or having alterations in the spacing between the sites indicate that the two delta elements function independently and contribute additively to the overall strength of the rpL32 promoter. Moreover, the contribution of the delta i element is the same whether it is oriented parallel or antiparallel to the delta e element. Together, the two delta elements raise the expression level about 10-fold over that attained by the upstream and initiator portions of the promoter. The positive role of the delta factor in rpL32 expression contrasts strikingly with its repressive role in various other genes.
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Affiliation(s)
- S Chung
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111
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10
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De Falco S, Russo G, Angiolillo A, Pietropaolo C. Human L7a ribosomal protein: sequence, structural organization, and expression of a functional gene. Gene X 1993; 126:227-35. [PMID: 8482538 DOI: 10.1016/0378-1119(93)90371-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A cDNA coding for the human L7a ribosomal protein (r-protein) was used to isolate the corresponding gene by screening two human genomic libraries constructed in bacteriophage lambda and in a cosmid vector. One of the cosmid clones isolated, cos1.1, contains the whole L7 alpha gene, composed of eight exons and seven introns spanning 3226 bp. As in other mammalian housekeeping genes, the promoter and the first exon of the L7 alpha reside within a CpG-rich island. Furthermore, similar to the other higher eukaryote r-protein-encoding genes characterized so far, the human L7 alpha gene has a C as the major transcriptional start point localized in a pyrimidine-rich region and lacks a canonical TATA sequence. We show that 130 bp of the human L7 alpha gene 5'-flanking region represent the minimal element required to promote its transcription. This element is strikingly conserved between the mouse and human L7 alpha genes. Finally, a comparison of the human L7 alpha gene coding sequence and the predicted amino acid (aa) sequence with the sequences of mouse L7a, rat L7a, and the homologous yeast L4 shows that the aa sequence has been highly conserved during evolution.
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Affiliation(s)
- S De Falco
- Dipartimento di Biochimica e Biotecnologie Mediche, Facoltà di Medicina e Chirurgia, Università di Napoli Federico II, Italy
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11
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Pata I, Hoth S, Kruppa J, Metspalu A. The human ribosomal protein S6 gene: isolation, primary structure and location in chromosome 9. Gene 1992; 121:387-92. [PMID: 1446836 DOI: 10.1016/0378-1119(92)90149-j] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Using PCR cloning we isolated the first intron of the human ribosomal protein S6 gene (hRPS6). By screening the human HeLa cell cDNA library in lambda ZAPII vector (Stratagene, La Jolla, CA), we identified and sequenced a partially spliced pre mRNA copy of hRPS6. The complete hRPS6 gene was isolated from a lambda DASH library with an intron-specific probe. The gene and flanking regions were sequenced, and the mRNA 5' end was mapped by primer extension experiments. The hRPS6 gene has 6 exons and 5 introns and is 3.6 kb long. Using intron-specific primers in PCR and a panel of human-hamster cell lines we localized the hRPS6 gene in human chromosome 9.
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Affiliation(s)
- I Pata
- Estonian Biocenter, Tartu, Estonia
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12
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Takasawa S, Tohgo A, Unno M, Shiga K, Yonekura H, Okamoto H. The primary structure of rat rig/ribosomal protein S15 gene. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1132:228-30. [PMID: 1390896 DOI: 10.1016/0167-4781(92)90020-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have isolated rat rig/ribosomal protein S15 gene from a DNA library derived from a rat insulinoma and determined the complete nucleotide sequence. The rat rig/S15 gene is composed of four exons and three introns spanning 2 kbp and exhibits distinctive structural features unique for a ribosomal protein gene.
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Affiliation(s)
- S Takasawa
- Department of Biochemistry, Tohoku University School of Medicine, Sendai, Japan
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13
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Yoganathan T, Horikoshi M, Hasegawa S, Roeder RG, Sells BH. Yeast transcription factor IID participates in cell-free transcription of a mammalian ribosomal protein TATA-less promoter. Biochem J 1992; 285 ( Pt 3):721-3. [PMID: 1497610 PMCID: PMC1132854 DOI: 10.1042/bj2850721] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We analysed transcription of the gene for the ribosomal protein (rp) L32 of the mouse, which is transcribed in mouse L1210 nuclear extracts in vitro. The rpL32 gene lacks a canonical TATA box. Hence it has been suggested that this gene has an alternative transcription pathway not requiring transcription factor IID (TFIID). Selective inactivation of TFIID in nuclear extract completely abolished the transcription of rpL32 in vitro. Selective inactivation was restored by the addition of cloned and purified yeast TFIID (yTFIID), indicating that this TATA-less rpL32 promoter utilizes TFIID for its transcription initiation. Furthermore, addition of an oligonucleotide-containing TATA sequence interfered with the rpL32 transcription and this was overcome by the addition of yTFIID. To further examine the stage of involvement of TFIID in rpL32 transcription, TATA oligonucleotide was added to nuclear extract before and after the formation of the transcription complex. The results reveal that TFIID associates with the pre-initiation complex and that this complex is largely resistant to added TATA oligonucleotide. Our results show, for the first time, that the TATA-less rpL32 gene utilizes TFIID for transcription initiation.
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Affiliation(s)
- T Yoganathan
- Department of Molecular Biology and Genetics, College of Biological Science, University of Guelph, Ontario, Canada
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14
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Colombo P, Fried M. Functional elements of the ribosomal protein L7a (rpL7a) gene promoter region and their conservation between mammals and birds. Nucleic Acids Res 1992; 20:3367-73. [PMID: 1630908 PMCID: PMC312491 DOI: 10.1093/nar/20.13.3367] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The transcriptional initiation sites of the chicken ribosomal protein L7a (rpL7a) gene have been determined and found to occur at three consecutive cytidine residues at the start of a polypyrimidine tract of 8 base pairs (bp). A comparative analysis of the 5' upstream regions of the mouse, human and chicken rpL7a genes identified two sequence elements (Box A and Box B) conserved over the 600 million years of divergent evolution that separate mammals and birds. Only Box A (nts - 56 to - 39) and Box B (nts - 25 to - 4) sequences were detected to bind nuclear factors from mouse nuclear extracts in an analysis of the mouse rpL7a 5' upstream sequence. Box A and Box B bind different nuclear factors and the factor binding to mouse Box A and mouse Box B sequences could be effectively competed by corresponding homologous sequences from the human and chicken rpL7a promoters. These results indicate that elements of the rpL7a promoter region are conserved between mammals and birds. An in vivo analysis of the mouse rpL7a 5' upstream sequence required for efficient transcription identified the 5' border of the minimal promoter region as lying between nts - 50 and - 56. Constructs containing 56 bp of 5' upstream DNA and the first 25 bp rpL7a exon were very efficiently transcribed indicating that sequences within the first intron are not required for gene expression. No sequence similarity was detected between the rpL7a promoter elements and described promoter elements of other eukaryotic ribosomal protein genes.
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Affiliation(s)
- P Colombo
- Eukaryotic Gene Organization and Expression Laboratory, Imperial Cancer Research Fund, London, UK
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15
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Larsen F, Gundersen G, Prydz H. Choice of enzymes for mapping based on CpG islands in the human genome. ACTA ACUST UNITED AC 1992; 9:80-5. [PMID: 1362073 DOI: 10.1016/1050-3862(92)90002-m] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The frequencies of sites for rare-cutting restriction enzymes in 2.9 million bp of human genomic DNA sequence in the EMBL database have been determined and compared with the expected frequencies. Rare cutters can be divided into four groups based on certain features of their recognition sites. Mlu, I, Nru I, Spl I, and Pvu I are predicted to cleave genomic DNA most infrequently, which is borne out by the fragment lengths observed for Mlu I and Nru I. Thus, these four enzymes are ideal for making long-range maps based on pulsed-field electrophoresis. Other enzymes like Not I are useful for making more detailed maps. Finer maps for identification of CpG islands and associated genes should involve several rare cutters including Eag I, Sac II and Bss HII. A cluster of sites for at least two such enzymes is a good indicator of a CpG island, and 78% of the island-associated genes can be located in this way.
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Affiliation(s)
- F Larsen
- Biotechnology Center of Oslo, University of Oslo, Norway
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16
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Abstract
The quantitative changes in the mRNAs for ribosomal proteins L7a, L18a, and S15 were assayed in slot hybridization experiments using labeled cRNA probes with total RNA from late growth-phase oocytes, ovulated eggs, and early embryos through the blastocyst stage. All three mRNAs showed a similar developmental pattern of prevalence, but their copy numbers per oocyte or embryo fluctuated according to developmental stage. There are on an average about 17,000 copies of each mRNA in the late growth-phase oocyte; this number drops to one-fifth to one-tenth in the ovulated egg and two-cell embryo but increases rapidly during cleavage to bout 25,000 in the eight-cell embryo and about 42,000 in the blastocyst. A comparison of the levels of these mRNAs with the reported rates of ribosomal protein synthesis (LaMarca and Wassarman, 1979) suggests that, in late growth-phase oocytes, ribosomal protein synthesis is regulated primarily at the translational level and is kept low by some factor limiting mRNA utilization. On the other hand, the high rate of ribosome biosynthesis during early embryogenesis from the two-cell stage onward appears to involve the coordinate activation and transcription of ribosomal RNA and ribosomal protein genes coupled with the immediate translational utilization of ribosomal protein mRNAs.
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Affiliation(s)
- K D Taylor
- Developmental Biology Laboratory, VA Medical Center, Sepulveda, California 91343
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17
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Doorenbosch T, Mager WH, Planta RJ. Multifunctional DNA-binding proteins in yeast. Gene Expr 1992; 2:193-201. [PMID: 1450661 PMCID: PMC6057378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- T Doorenbosch
- Department of Biochemistry and Molecular Biology, Free University, Amsterdam, The Netherlands
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18
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Colombo P, Yon J, Fried M. The organization and expression of the human L7a ribosomal protein gene. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1129:93-5. [PMID: 1756182 DOI: 10.1016/0167-4781(91)90218-b] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The genomic structure and sequence of the human ribosomal protein L7a (rpL7a) and its transcriptional start sites have been determined. The gene contains eight exons and seven introns spread over 3179 bp. The human rpL7a gene is similar to other mammalian ribosomal protein genes in containing a short first exon, a short 5' untranslated leader and its transcriptional start sites at C residues embedded in a polypyrimidine tract. The 25 bp polypyrimidine tract containing the two human rpL7a start sites is the longest polypyrimide tract so far observed for a mammalian ribosomal protein gene.
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Affiliation(s)
- P Colombo
- Department of Eukaryotic Gene Organization and Expression, Imperial Cancer Research Fund, London, U.K
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Chan YL, Wool IG. The structure of a gene containing introns and encoding rat ribosomal protein P2. Nucleic Acids Res 1991; 19:4895-900. [PMID: 1923757 PMCID: PMC328786 DOI: 10.1093/nar/19.18.4895] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The single rat ribosomal protein P2 gene containing introns has been characterized. It has 2275 nucleotides distributed in 5 exons and 4 introns. The sequence of amino acids encoded in the exons corresponds exactly to that derived before from a cDNA. Only this one P2 gene in a family of approximately 9 members has introns and is expressed. There are two transcriptional start sites (adjacent cytidine residues) located in a tract of 10 pyrimidines flanked by GC-rich regions. The P2 gene, like other mammalian ribosomal protein genes, lacks a TATA box; however, it has at positions -30 to -27 the sequence TTTA which may be a degenerate TATA box and may serve the same function. The architecture of the P2 gene, and especially the structure of the promoter region, resembles that of other mammalian ribosomal protein genes. This suggests that the common features contribute to the coordinate regulation of their transcription and that the stoichiometry of P2 (it is present in 2 copies in the ribosome) is achieved by regulation of the translation of its mRNA.
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Affiliation(s)
- Y L Chan
- Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637
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Levy S, Avni D, Hariharan N, Perry RP, Meyuhas O. Oligopyrimidine tract at the 5' end of mammalian ribosomal protein mRNAs is required for their translational control. Proc Natl Acad Sci U S A 1991; 88:3319-23. [PMID: 2014251 PMCID: PMC51438 DOI: 10.1073/pnas.88.8.3319] [Citation(s) in RCA: 265] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Mammalian ribosomal protein (rp) mRNAs are subject to translational control, as illustrated by their selective release from polyribosomes in growth-arrested cells and their underrepresentation in polysomes in normally growing cells. In the present experiments, we have examined whether the translational control of rp mRNAs is attributable to the distinctive features of their 5' untranslated region, in particular to the oligopyrimidine tract adjacent to the cap structure. Murine lymphosarcoma cells were transfected with chimeric genes consisting of selected regions of rp mRNA fused to non-rp mRNA segments, and the translational efficiency of the resulting chimeric mRNAs was assessed in cells that either were growing normally or were growth-arrested by glucocorticoid treatment. We observed that translational control of rpL32 mRNA was abolished when its 5' untranslated region was replaced by that of beta-actin. At the same time, human growth hormone (hGH) mRNA acquired the typical behavior of rp mRNAs when it was preceded by the first 61 nucleotides of rpL30 mRNA or the first 29 nucleotides of rpS16 mRNA. Moreover, the translational control of rpS16-hGH mRNA was abolished by the substitution of purines into the pyrimidine tract or by shortening it from eight to six residues with a concomitant cytidine----uridine change at the 5' terminus. These results indicate that the 5'-terminal pyrimidine tract plays a critical role in the translational control mechanism. Possible factors that might interact with this translational cis regulatory element are discussed.
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Affiliation(s)
- S Levy
- Department of Developmental Biochemistry, Hebrew University-Hadassah Medical School, Jerusalem, Israel
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Baker RT, Board PG. The human ubiquitin-52 amino acid fusion protein gene shares several structural features with mammalian ribosomal protein genes. Nucleic Acids Res 1991; 19:1035-40. [PMID: 1850507 PMCID: PMC333777 DOI: 10.1093/nar/19.5.1035] [Citation(s) in RCA: 117] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Complementary DNA clones encoding ubiquitin fused to a 52 amino acid tail protein were isolated from human placental and adrenal gland cDNA libraries. The deduced human 52 amino acid tail protein is very similar to the homologous protein from other species, including the conservation of the putative metal-binding, nucleic acid-binding domain observed in these proteins. Northern blot analysis with a tail-specific probe indicated that the previously identified UbA mRNA species most likely represents comigrating transcripts of the 52 amino acid tail (UbA52) and 80 amino acid tail (UbA80) ubiquitin fusion genes. The UbA52 gene was isolated from a human genomic library and consists of five exons distributed over 3400 base pairs. One intron is in the 5' non-coding region, two interrupt the single ubiquitin coding unit, and the fourth intron is within the tail coding region. Several members of the Alu family of repetitive DNA are associated with the gene. The UbA52 promoter has several features in common with mammalian ribosomal protein genes, including its location in a CpG-rich island, initiation of transcription within a polypyrimidine tract, the lack of a consensus TATA motif, and the presence of Sp1 binding sites, observations that are consistent with the recent identification of the ubiquitin-free tail proteins as ribosomal proteins. Thus, in spite of its unusual feature of being translationally fused to ubiquitin, the 52 amino acid tail ribosomal protein is expressed from a structurally typical ribosomal protein gene.
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Affiliation(s)
- R T Baker
- Human Genetics Group, John Curtin School of Medical Research, Australian National University, Canberra
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New nucleotide sequence data on the EMBL file server. Nucleic Acids Res 1990; 18:7201-7. [PMID: 2263510 PMCID: PMC332850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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