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Scherrer K. Primary transcripts: From the discovery of RNA processing to current concepts of gene expression - Review. Exp Cell Res 2018; 373:1-33. [PMID: 30266658 DOI: 10.1016/j.yexcr.2018.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 12/15/2022]
Abstract
The main purpose of this review is to recall for investigators - and in particular students -, some of the early data and concepts in molecular genetics and biology that are rarely cited in the current literature and are thus invariably overlooked. There is a growing tendency among editors and reviewers to consider that only data produced in the last 10-20 years or so are pertinent. However this is not the case. In exact science, sound data and lucid interpretation never become obsolete, and even if forgotten, will resurface sooner or later. In the field of gene expression, covered in the present review, recent post-genomic data have indeed confirmed many of the earlier results and concepts developed in the mid-seventies, well before the start of the recombinant DNA revolution. Human brains and even the most powerful computers, have difficulty in handling and making sense of the overwhelming flow of data generated by recent high-throughput technologies. This was easier when low throughput, more integrative methods based on biochemistry and microscopy dominated biological research. Nowadays, the need for organising concepts is ever more important, otherwise the mass of available data can generate only "building ruins" - the bricks without an architect. Concepts such as pervasive transcription of genomes, large genomic domains, full domain transcripts (FDTs) up to 100 kb long, the prevalence of post-transcriptional events in regulating eukaryotic gene expression, and the 3D-genome architecture, were all developed and discussed before 1990, and are only now coming back into vogue. Thus, to review the impact of earlier concepts on later developments in the field, I will confront former and current data and ideas, including a discussion of old and new methods. Whenever useful, I shall first briefly report post-genomic developments before addressing former results and interpretations. Equally important, some of the terms often used sloppily in scientific discussions will be clearly defined. As a basis for the ensuing discussion, some of the issues and facts related to eukaryotic gene expression will first be introduced. In chapter 2 the evolution in perception of biology over the last 60 years and the impact of the recombinant DNA revolution will be considered. Then, in chapter 3 data and theory concerning the genome, gene expression and genetics will be reviewed. The experimental and theoretical definition of the gene will be discussed before considering the 3 different types of genetic information - the "Triad" - and the importance of post-transcriptional regulation of gene expression in the light of the recent finding that 90% of genomic DNA seems to be transcribed. Some previous attempts to provide a conceptual framework for these observations will be recalled, in particular the "Cascade Regulation Hypothesis" (CRH) developed in 1967-85, and the "Gene and Genon" concept proposed in 2007. A knowledge of the size of primary transcripts is of prime importance, both for experimental and theoretical reasons, since these molecules represent the primary units of the "RNA genome" on which most of the post-transcriptional regulation of gene expression occurs. In chapter 4, I will first discuss some current post-genomic topics before summarising the discovery of the high Mr-RNA transcripts, and the investigation of their processing spanning the last 50 years. Since even today, a consensus concerning the real form of primary transcripts in eukaryotic cells has not yet been reached, I will refer to the viral and specialized cellular models which helped early on to understand the mechanisms of RNA processing and differential splicing which operate in cells and tissues. As a well-studied example of expression and regulation of a specific cellular gene in relation to differentiation and pathology, I will discuss the early and recent work on expression of the globin genes in nucleated avian erythroblasts. An important concept is that the primary transcript not only embodies protein-coding information and regulation of its expression, but also the 3D-structure of the genomic DNA from which it was derived. The wealth of recent post-genomic data published in this field emphasises the importance of a fundamental principle of genome organisation and expression that has been overlooked for years even though it was already discussed in the 1970-80ties. These issues are addressed in chapter 5 which focuses on the involvement of the nuclear matrix and nuclear architecture in DNA and RNA biology. This section will make reference to the Unified Matrix Hypothesis (UMH), which was the first molecular model of the 3D organisation of DNA and RNA. The chapter on the "RNA-genome and peripheral memories" discusses experimental data on the ribonucleoprotein complexes containing pre-mRNA (pre-mRNPs) and mRNA (mRNPs) which are organised in nuclear and cytoplasmic spaces respectively. Finally, "Outlook " will enumerate currently unresolved questions in the field, and will propose some ideas that may encourage further investigation, and comprehension of available experimental data still in need of interpretation. In chapter 8, some propositions and paradigms basic to the authors own analysis are discussed. "In conclusion" the raison d'être of this review is recalled and positioned within the overall framework of scientific endeavour.
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Affiliation(s)
- Klaus Scherrer
- Institute Jacques Monod, CNRS, University Paris Diderot, Paris, France.
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Scherrer K, Jost J. Gene and genon concept: coding versus regulation. A conceptual and information-theoretic analysis of genetic storage and expression in the light of modern molecular biology. Theory Biosci 2007; 126:65-113. [PMID: 18087760 PMCID: PMC2242853 DOI: 10.1007/s12064-007-0012-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 07/13/2007] [Indexed: 01/15/2023]
Abstract
We analyse here the definition of the gene in order to distinguish, on the basis of modern insight in molecular biology, what the gene is coding for, namely a specific polypeptide, and how its expression is realized and controlled. Before the coding role of the DNA was discovered, a gene was identified with a specific phenotypic trait, from Mendel through Morgan up to Benzer. Subsequently, however, molecular biologists ventured to define a gene at the level of the DNA sequence in terms of coding. As is becoming ever more evident, the relations between information stored at DNA level and functional products are very intricate, and the regulatory aspects are as important and essential as the information coding for products. This approach led, thus, to a conceptual hybrid that confused coding, regulation and functional aspects. In this essay, we develop a definition of the gene that once again starts from the functional aspect. A cellular function can be represented by a polypeptide or an RNA. In the case of the polypeptide, its biochemical identity is determined by the mRNA prior to translation, and that is where we locate the gene. The steps from specific, but possibly separated sequence fragments at DNA level to that final mRNA then can be analysed in terms of regulation. For that purpose, we coin the new term "genon". In that manner, we can clearly separate product and regulative information while keeping the fundamental relation between coding and function without the need to introduce a conceptual hybrid. In mRNA, the program regulating the expression of a gene is superimposed onto and added to the coding sequence in cis - we call it the genon. The complementary external control of a given mRNA by trans-acting factors is incorporated in its transgenon. A consequence of this definition is that, in eukaryotes, the gene is, in most cases, not yet present at DNA level. Rather, it is assembled by RNA processing, including differential splicing, from various pieces, as steered by the genon. It emerges finally as an uninterrupted nucleic acid sequence at mRNA level just prior to translation, in faithful correspondence with the amino acid sequence to be produced as a polypeptide. After translation, the genon has fulfilled its role and expires. The distinction between the protein coding information as materialised in the final polypeptide and the processing information represented by the genon allows us to set up a new information theoretic scheme. The standard sequence information determined by the genetic code expresses the relation between coding sequence and product. Backward analysis asks from which coding region in the DNA a given polypeptide originates. The (more interesting) forward analysis asks in how many polypeptides of how many different types a given DNA segment is expressed. This concerns the control of the expression process for which we have introduced the genon concept. Thus, the information theoretic analysis can capture the complementary aspects of coding and regulation, of gene and genon.
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Affiliation(s)
- Klaus Scherrer
- Institut Jacques Monod, CNRS and Univ. Paris 7, 2, place Jussieu, 75251 Paris-Cedex 5, France
| | - Jürgen Jost
- Max Planck Institute for Mathematics in the Sciences MPI MIS, Inselstrasse 22, 04103 Leipzig, Germany
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Scherrer K, Jost J. The gene and the genon concept: a functional and information-theoretic analysis. Mol Syst Biol 2007; 3:87. [PMID: 17353929 PMCID: PMC1847941 DOI: 10.1038/msb4100123] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Accepted: 12/21/2006] [Indexed: 01/21/2023] Open
Abstract
'Gene' has become a vague and ill-defined concept. To set the stage for mathematical analysis of gene storage and expression, we return to the original concept of the gene as a function encoded in the genome, basis of genetic analysis, that is a polypeptide or other functional product. The additional information needed to express a gene is contained within each mRNA as an ensemble of signals, added to or superimposed onto the coding sequence. To designate this programme, we introduce the term 'genon'. Individual genons are contained in the pre-mRNA forming a pre-genon. A genomic domain contains a proto-genon, with the signals of transcription activation in addition to the pre-genon in the transcripts. Some contain several mRNAs and hence genons, to be singled out by RNA processing and differential splicing. The programme in the genon in cis is implemented by corresponding factors of protein or RNA nature contained in the transgenon of the cell or organism. The gene, the cis programme contained in the individual domain and transcript, and the trans programme of factors, can be analysed by information theory.
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Affiliation(s)
- Klaus Scherrer
- Institut Jacques Monod, CNRS and Univ. Paris 7, Paris, France
| | - Jürgen Jost
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
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Abstract
Translational control is a prevalent means of gene regulation during Drosophila oogenesis and embryogenesis. Multiple maternal mRNAs are localized within the oocyte, and this localization is often coupled to their translational regulation. Subsequently, translational control allows maternally deposited mRNAs to direct the early stages of embryonic development. In this review we outline some general mechanisms of translational regulation and mRNA localization that have been uncovered in various model systems. Then we focus on the posttranscriptional regulation of four maternal transcripts in Drosophila that are localized during oogenesis and are critical for embryonic patterning: bicoid (bcd), nanos (nos), oskar (osk), and gurken (grk). Cis- and trans-acting factors required for the localization and translational control of these mRNAs are discussed along with potential mechanisms for their regulation.
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Affiliation(s)
- O Johnstone
- Department of Biology, McGill University, 1205 Avenue Docteur Penfield, Montréal, Québec, H3A 1B1 Canada.
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Abstract
Translation processes in plants are very similar to those in other eukaryotic organisms and can in general be explained with the scanning model. Particularly among plant viruses, unconventional mRNAs are frequent, which use modulated translation processes for their expression: leaky scanning, translational stop codon readthrough or frameshifting, and transactivation by virus-encoded proteins are used to translate polycistronic mRNAs; leader and trailer sequences confer (cap-independent) efficient ribosome binding, usually in an end-dependent mechanism, but true internal ribosome entry may occur as well; in a ribosome shunt, sequences within an RNA can be bypassed by scanning ribosomes. Translation in plant cells is regulated under conditions of stress and during development, but the underlying molecular mechanisms have not yet been determined. Only a small number of plant mRNAs, whose structure suggests that they might require some unusual translation mechanisms, have been described.
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Affiliation(s)
- J Fütterer
- Institute of Plant Sciences, ETHZ, Zürich, Switzerland
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Scherrer K, Bey F. The prosomes (multicatalytic proteinases; proteasomes) and their relationship to the untranslated messenger ribonucleoproteins, the cytoskeleton, and cell differentiation. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1994; 49:1-64. [PMID: 7863004 DOI: 10.1016/s0079-6603(08)60047-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- K Scherrer
- Institute Jacques Monod CNRS, Paris, France
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Abstract
To evaluate the hypothesis that the 3' poly(A) tract of mRNA plays a role in translational initiation, we constructed derivatives of pSP65 which direct the in vitro synthesis of mRNAs with different poly(A) tail lengths and compared, in reticulocyte extracts, the relative efficiencies with which such mRNAs were translated, degraded, recruited into polysomes, and assembled into messenger ribonucleoproteins or intermediates in the translational initiation pathway. Relative to mRNAs which were polyadenylated, we found that nonpolyadenylated [poly(A)-]mRNAs had a reduced translational capacity which was not due to an increase in their decay rates, but was attributable to a reduction in their efficiency of recruitment into polysomes. The defect in poly(A)- mRNAs affected a late step in translational initiation, was distinct from the phenotype associated with cap-deficient mRNAs, and resulted in a reduced ability to form 80S initiation complexes. Moreover, poly(A) added in trans inhibited translation from capped polyadenylated mRNAs but stimulated translation from capped poly(A)- mRNAs. We suggest that the presence of a 3' poly(A) tail may facilitate the binding of an initiation factor or ribosomal subunit at the mRNA 5' end.
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Abstract
Until recently, evidence to support a translational role for the 3'-poly(A) tract of eukaryotic mRNAs has been mostly indirect, including: a correlation between the adenylation status of individual mRNAs and their translatability in vivo or in vitro, the demonstration that exogenously added poly(A) is a potent competitive inhibitor of the translation of poly(A)+mRNA, but not poly(A)-mRNAs in vitro, and a correlation between the abundance and stability of poly(A)-binding proteins (PABPs) and the rate of translational initiation in vivo. However, more recent studies demonstrate directly that poly(A)+mRNAs can initiate translation more efficiently than poly(A)-mRNAs, and indicate that this effect is: (i) targeted to the formation of 80S initiation complexes, and (ii) likely to be mediated by the cytoplasmic PABP. We suggest that the 3'-poly(A) tail should be considered a translational enhancer which may stimulate translational initiation in much the same way that transcriptional enhancers are thought to stimulate transcriptional initiation.
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Affiliation(s)
- D Munroe
- Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester 01655
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Abstract
To evaluate the hypothesis that the 3' poly(A) tract of mRNA plays a role in translational initiation, we constructed derivatives of pSP65 which direct the in vitro synthesis of mRNAs with different poly(A) tail lengths and compared, in reticulocyte extracts, the relative efficiencies with which such mRNAs were translated, degraded, recruited into polysomes, and assembled into messenger ribonucleoproteins or intermediates in the translational initiation pathway. Relative to mRNAs which were polyadenylated, we found that nonpolyadenylated [poly(A)-]mRNAs had a reduced translational capacity which was not due to an increase in their decay rates, but was attributable to a reduction in their efficiency of recruitment into polysomes. The defect in poly(A)- mRNAs affected a late step in translational initiation, was distinct from the phenotype associated with cap-deficient mRNAs, and resulted in a reduced ability to form 80S initiation complexes. Moreover, poly(A) added in trans inhibited translation from capped polyadenylated mRNAs but stimulated translation from capped poly(A)- mRNAs. We suggest that the presence of a 3' poly(A) tail may facilitate the binding of an initiation factor or ribosomal subunit at the mRNA 5' end.
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Affiliation(s)
- D Munroe
- Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester 01655
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Schröder HC, Diehl-Seifert B, Rottmann M, Messer R, Bryson BA, Agutter PS, Müller WE. Functional dissection of nuclear envelope mRNA translocation system: effects of phorbol ester and a monoclonal antibody recognizing cytoskeletal structures. Arch Biochem Biophys 1988; 261:394-404. [PMID: 2895607 DOI: 10.1016/0003-9861(88)90355-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Unidirectional transport of poly(A)-containing mRNA [poly(A)+ mRNA] through the nuclear envelope pore complex is thought to be an energy (ATP or GTP)-dependent process which involves a nuclear envelope nucleoside triphosphatase (NTPase). In the intact envelope, this enzyme is regulatable by poly(A) binding and by poly(A)-dependent phosphorylation/dephosphorylation of other components of the mRNA translocation system, which are as yet unidentified. Monoclonal antibodies (mAbs) were elicited against the poly(A) binding nuclear envelope fraction isolated from rat liver. The mAbs were screened for their modulatory effects on mRNA transport in vitro. One stable clone decreased the efflux of rapidly labeled RNA and of one specific mRNA (ovalbumin) from isolated nuclei. It increased the binding of poly(A) to the envelope and increased the maximal catalytic rate of the NTPase, but it did not alter the apparent Km of the enzyme or the extent of its stimulation by poly(A). The nuclear envelope-associated protein kinase that down-regulates the NTPase was inhibited by the antibody, while other protein kinases were not affected. Because both the NTPase and mRNA efflux were inhibited by the tumor promoter, 12-O-tetradecanoylphorbol 13-acetate, the sensitive kinase is probably protein kinase C. Protein kinase C was found to be associated with the isolated nuclear envelope. The antibody reacted with both a Mr 83,000 and a Mr 65,000 nuclear envelope polypeptide from rat liver and other tissues. By immunofluorescence microscopy in CV-1 cells, the antibody localized to the nuclear envelope and, in addition, to cytoplasmic filaments which show some superposition with the microfilament network.
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Affiliation(s)
- H C Schröder
- Institut für Physiologische Chemie, Universität, Mainz, Federal Republic of Germany
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Nucleo-Cytoplasmic Transport of mRNA: Its Relationship to RNA Metabolism, Subcellular Structures and Other Nucleocytoplasmic Exchanges. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 1988. [DOI: 10.1007/978-3-642-73599-8_2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Abstract
Specific proteins are associated with mRNA in the cytoplasm of eukaryotic cells. The complement of associated proteins depends upon whether the mRNA is an integral component of the polysomal complex being translated, or, alternatively, whether it is part of the non-translated free mRNP fraction. By subjecting cells to ultraviolet irradiation in vivo to cross-link proteins to mRNA, mRNP proteins have been shown to be associated with specific regions of the mRNA molecule. Examination of mRNP complexes containing a unique mRNA has suggested that not all mRNA contain the same family of associated RNA binding proteins. The functions of mRNA associated proteins may include a role in providing stability for mRNA, and/or in modulating translation. With the recent demonstrations that both free and polysomal mRNPs are associated with the cytoskeletal framework, specific mRNP proteins may play a role in determining the subcellular localization of specific mRNPs.
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Schröder HC, Bachmann M, Diehl-Seifert B, Müller WE. Transport of mRNA from nucleus to cytoplasm. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1987; 34:89-142. [PMID: 3326042 DOI: 10.1016/s0079-6603(08)60494-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Lockard RE, Currey K, Browner M, Lawrence C, Maizel J. Secondary structure model for mouse beta Maj globin mRNA derived from enzymatic digestion data, comparative sequence and computer analysis. Nucleic Acids Res 1986; 14:5827-41. [PMID: 3737415 PMCID: PMC311594 DOI: 10.1093/nar/14.14.5827] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A model for the secondary structure of mouse beta Maj globin messenger RNA is presented based on enzymatic digestion data, comparative sequence and computer analysis. Using 5'-32P-end-labeled beta globin mRNA as a substrate, single-stranded regions were determined with S1 and T1 nucleases and double-stranded regions with V1 ribonuclease from cobra venom. The structure data obtained for ca. 75% of the molecule was introduced into a computer algorithm which predicts secondary structures of minimum free energy consistent with the enzymatic data. Two prominent base paired regions independently derived by phylogenetic analysis were also present in the computer generated structure lending support for the model. An interesting feature of the model is the presence of long-range base pairing interactions which permit the beta globin mRNA to fold back on itself, thereby bringing the 5'- and 3'-noncoding regions within close proximity. This feature is consistent with data from other laboratories suggesting an interaction of the 5'- and 3'-domains in the mammalian globin mRNAs.
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Martins de Sa C, Grossi de Sa MF, Akhayat O, Broders F, Scherrer K, Horsch A, Schmid HP. Prosomes. Ubiquity and inter-species structural variation. J Mol Biol 1986; 187:479-93. [PMID: 2423694 DOI: 10.1016/0022-2836(86)90328-1] [Citation(s) in RCA: 109] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The "prosomes", a novel type of ubiquitous ribonucleoprotein particle of extraordinary stability and of defined electron microscopical structure, have been characterized in several cell types and species. Identified as a 19 S sub-component of free mRNA-protein complexes, including globin and other repressed mRNA, in the cytoplasm of duck, mouse and HeLa cells, they were previously found to inhibit protein synthesis in vitro. In all cells studied, electron microscopy shows an identical, seemingly ring-like but rather raspberry-shaped particle of 12 nm diameter, resistant to EDTA and 1% (w/v) Sarkosyl. Two-dimensional electrophoretic analysis of prosomal proteins shows a characteristic pattern in the 19,000 to 35,000 Mr range of pI 4 to 7, with an additional 56,000 Mr component specific to avian species. The prosomes found in globin mRNA-protein complexes contain about 25 protein components, 16 of which have identical molecular weight and pI values in duck and mouse, and which are also found in the prosomes of the heterogeneous free mRNPs of HeLa cells. Seral and monoclonal antibodies raised in mice against the prosomes of duck erythroblasts cross-react with some of the proteins of the mouse and HeLa cell particles. Prosomes isolated from duck and mouse globin mRNP, both contain small cytoplasmic RNAs of 70 to 90 nucleotides, which represent about 15% of the particle mass. The molecular weight and the 3'-terminal oligonucleotide of each one of these small cytoplasmic RNAs are identical in the two animal species; fingerprints of their oligonucleotides generated by RNase T1 show that more than 80% of spots are identical. In contrast, the prosomes of HeLa cells, associated with a large population of repressed mRNA, contain at least 12 small cytoplasmic RNA species. All prosomal RNAs tested so far hybridize to mRNA. The data available indicate that prosomes constitute a novel class of ubiquitous cellular ribonucleoprotein complexes, present in the nucleus and cytoplasm that, in its structural variations shown here, reflects function and species.
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Vincent A, Goldenberg S, Standart N, Civelli O, Imaizumi-Scherrer T, Maundrell K, Scherrer K. Potential role of mRNP proteins in cytoplasmic control of gene expression in duck erythroblasts. Mol Biol Rep 1981; 7:71-81. [PMID: 6114396 DOI: 10.1007/bf00778736] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Ladhoff AM, Uerlings I, Rosenthal S. Electron microscopic evidence of circular molecules in 9-S globin mRNA from rabbit reticulocytes. Mol Biol Rep 1981; 7:101-6. [PMID: 7019667 DOI: 10.1007/bf00778739] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
9S globin mRNA prepared by the proteinase K method from polysomes of rabbit reticulocytes consists of 40% circular molecules as revealed by electron microscopy, if spreading of the molecules is performed from a solution of 50% formamide, 0.5 M NaCl, 25 mM Tris, 10 mM EDTA, pH 8, after 16 h incubation at 42 degrees C. We assume a noncovalent nature of the circularization because of the fact that a total transformation into the well known linear form occurs if strong denaturing conditions for spreading were used. The biological significance of the circular globin mRNA molecules is unknown.
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Moore RE, Sharma RK. Endogenous substrate for cyclic AMP-dependent protein kinase in adrenocortical polyadenylated messenger ribonucleoproteins. Science 1980; 210:1137-9. [PMID: 6255561 DOI: 10.1126/science.6255561] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
An endogenous polysomal cyclic AMP-dependent protein kinase specifically phosphorylates a 150,000-dalton peptide bound to an adrenocortical polyadenylated messenger ribonucleoprotein complex. There is a possibility that this protein is a physiological substrate of cyclic AMP-dependent protein kinase and that the phosphorylation and dephosphorylation of this substrate may be important in the translation control of adrenal polyadenylated messenger RNA.
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Goldenberg S, Vincent A, Scherrer K. Ribonucleotide sequences non-adjacent to poly(A) participate in the poly(A)-protein complex in 15S duck globin mRNP particles. Nucleic Acids Res 1980; 8:5057-70. [PMID: 7443531 PMCID: PMC324279 DOI: 10.1093/nar/8.21.5057] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The study of the interaction between mRNA and proteins in the polyribosomal 15 S duck globin messenger ribonucleoprotein complex showed that proteins protect specific mRNA sequences against digestion by the nonspecific micrococcal nuclease (Nucleic Acids Research 6 (8) 2787, 1979). Here we report the isolation of the poly(A)-protein RNP complex from nuclease digested 15 S mRNP by two different methods: sucrose gradient sedimentation and oligo(dT)-cellulose chromatography. We show by fingerprint analysis, that aprt from the periodically fragmented poly(A) segment, mRNA sequences adjacent and non-adjacent to the poly(A) segment are protected by the poly(A) binding proteins against nuclease digestion. The duck globin poly(A)-protein RNP complex, with a sedimentation coefficient between 7 S and 10 S, shows a characteristic protein composition, with a major 73,000 MW polypeptide and some minor components. The results are discussed in view of a dynamic ribonucleoprotein structure.
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Maundrell K, Maxwell ES, Civelli O, Vincent A, Goldenberg S, Buri JF, Imaizumi-Scherrer MT, Scherrer K. Messenger ribonucleoprotein complexes in avian erythroblasts: carriers of post-transcriptional regulation? Mol Biol Rep 1979; 5:43-51. [PMID: 379594 DOI: 10.1007/bf00777487] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Jeffery WR. Composition and properties of messenger ribonucleoprotein fragments containing and lacking polyadenylate. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 521:217-28. [PMID: 718927 DOI: 10.1016/0005-2787(78)90264-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ribonucleoprotein fragments were isolated from Ehrlich ascites cell messenger ribonucleoprotein (mRNP), immobilized on oligo(dT)-cellulose, by successive RNAase and formamide treatments and their RNA and protein moieties were characterized. A 8--10 S formamide-eluted (F) RNP primarily contained the poly(A) segment as an RNA moiety, as evidenced by its characteristic electrophoretic mobility, resistance to RNAase digestion, affinity for nitrocellulose filters and poly(U), and base composition. In contrast, the RNAase-eluted (R) fraction was composed of a 2--3 S RNP carrying a much shorter polyribonucleotide fragment of heterogeneous base composition and properties unlike poly(A). Sodium dodecyl sulfate-polyacrylamide electrophoresis indicated that the protein moieties of the R fraction were composed primarily of 56 000, 67 000, and 71 000 molecular weight polypeptides whereas those of the F fraction contained the latter three polypeptides as well as a major species exhibiting a molecular weight of 81 000. The data demonstrate that RNA sequences other than poly(A) interact with protein in mRNP, that three major mRNP polypeptides are associated with both poly(A) and non-poly(A) RNA binding sites, and that one major polypeptide is specifically bound to the poly-(A) region of mRNP.
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Preobrazhensky AA, Spirin AS. Informosomes and their protein components: the present state of knowledge. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1978; 21:1-38. [PMID: 358275 DOI: 10.1016/s0079-6603(08)60265-2] [Citation(s) in RCA: 146] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Chen JH, Lavers GC, Spector A. Calf lens messenger ribonucleoprotein complexes. Characterization and comparison of template activity with corresponding mRNAs. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 418:39-51. [PMID: 54193 DOI: 10.1016/0005-2787(76)90325-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Lens messenger ribonucleoprotein complexes have been isolated from calf lens polysomes by sucrose gradient centrifugation after puromycin-induced dissociation. A 10 S mRNA was released from a 13 S messenger ribonucleoprotein complex and a 14 S mRNA from a 19 S messenger ribonucleoprotein complex. Two major protein components with molecular weights of approx. 64 000 and 40 000 were isolated from each of the messenger ribonucleoprotein complexes after RNAase digestion. Buoyant density determinations suggest that the messenger ribonucleoprotein complexes contain approximately one mol of each major protein species per mol mRNA. In contrast to lens mRNA, lens messenger ribonucleoproteins are poor templates for transcription with avian myeloblastosis virus reverse transcriptase. Similar results were also obtained with globin messenger ribonucleoprotein containing either two major protein species (or deficient in the lower molecular weight protein species). Polynucleotide phosphorylase eliminates the reverse transcription template activity of the lens mRNA. This effect is blocked in the messenger ribonucleoprotein. Such observations suggest that at least one of the protein components associated with lens messenger ribonucleoprotein may be located in the 3'-terminal region. Only a small variation in translation activity was observed between the messenger ribonucleoproteins and their respective mRNAs.
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Ladhoff AM, Thiele BJ, Coutelle C. Precursor mRNA from erythroid-enriched bone-marrow cells of the rabbit. Electron microscope investigation of precursor mRNA molecules, molecular weight about 1.7 X 10(7), containing mRNA-like structures at one end. EUROPEAN JOURNAL OF BIOCHEMISTRY 1975; 58:431-8. [PMID: 1183445 DOI: 10.1111/j.1432-1033.1975.tb02390.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Precursor mRNA (pre-mRNA) molecules, sedimenting at greater than 45 S, from erythroid-enriched bone marrow cells of the rabbit and hemoglobin mRNA molecules from rabbit reticulocytes were investigated by electron microscopy. Four of 98 measured pre-mRNA molecules had a length between 15 and 17.1 mum. In some of the pre-mRNA molecules a characteristic condensed structure was observed at one end, strikingly resembling the structure of the mRNA molecules.
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Favre A, Morel C, Scherrer K. The secondary structure and poly(A) content of globin messenger RNA as a pure RNA and in polyribosome-derived ribonucleoprotein complexes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1975; 57:147-57. [PMID: 1175639 DOI: 10.1111/j.1432-1033.1975.tb02285.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The conformation in solution of duck and rabbit globin mRNA, and of the duck mRNA in the mRNA - protein particle, has been investigated by optical methods and also by the use of the dye ethidium bromide which becomes highly fluorescent when intercalated into the double-stranded regions of a nucleic acid. On the basis of the properties of this dye and on the ability of homopolyribonucleotides to form double-stranded structures we have, in addition, developed a simple and sensitive assay for the detection and quantitisation of sequences rich in a particular residue that may be present in an RNA chain. In solution, 45 to 60% of the nucleotides of duck globin nRNA were found to be in bihelical regions. A similar degree of secondary structure was found in rabbit globin mRNA (this paper), as well as in calf lens mRNA and mRNAs from ewe mammary gland (other results). All samples of globin mRNA examined in this work containeda sequence of poly(A), which has poly(U) binding properties similar to that of synthetic poly(a): no specific interaction between the poly(A) sequence and the rest of the molecules can be detected. The fraction of adenosine residues within these poly(A) segments represents 4% in rabbit mRNA and 8 to 9% in duck mRNA. An additional adenosine-rich segment interspersed with guanosine and possibly other residues, was also detected in one duck mRNA sample. The RNA in the duck mRNA - protein particle is also highly structured. The melting profile in the range of 20 to 65 degrees C is quite similar to that of free mRNA and the ability of ethidium bromide to intercalate is reduced to the extent of 70%. Yet the dichroic spectra of free and bound mRNA are significantly distinct. These data suggest that free and protein-bound mRNA May have a very similar degree of secondary structure but with distinct detailed conformation in bihelical regions (change in base tilting for example). Direct evidence has been obtained that proteins stick to the poly(A) segment in the particle since the fraction of adenosine residues detectable by our poly(u) titration procedure is reduced to 50% of that observed in the free mRNA.
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Viscardi RC, Ozaki LS, Morel C. Different sensitivities of avian- and mammalian-haemoglobin synthesis to elevated temperatures. Mol Biol Rep 1975; 2:41-7. [PMID: 1128516 DOI: 10.1007/bf00357296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Avian- and mammalian-haemoglobin synthesis show different sensitivities to elevated temperatures. Temperature-dependent, reversible polyribosome disaggregation in avian cells occurs only at 45 degrees C, which is 3 degrees higher than the temperature for mammalian cells, and seems to be due to a block in the initiation of new polypeptide chains. The implications of these findings are discussed.
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Gasaryan KG, Tarantul VZ, Baranov YU, Frolova LY, Kisselev LL. Elements of the secondary structure in the DNA, complementary to pigeon globin mRNA. Mol Biol Rep 1974; 1:465-70. [PMID: 4141751 DOI: 10.1007/bf00360673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Abstract
Dark-field electron micrographs of aldehyde-fixed, unstained yeast-phase cells of Trichosporon cutaneum exhibit remarkable contrast and good resolution when the sections studied are less than 25 nm thick and conical illumination is used.
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Scherrer K. Control of gene expression in animal cells: the cascade regulation hypothesis revisited. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1974; 44:169-219. [PMID: 4601260 DOI: 10.1007/978-1-4684-3246-6_13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Morel C, Gander ES, Herzberg M, Dubochet J, Scherrer K. The duck-globin messenger-ribonucleoprotein complex. Resistance to high ionic strength, particle gel electrophoresis, composition and visualisation by dark-field electron microscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 36:455-64. [PMID: 4738397 DOI: 10.1111/j.1432-1033.1973.tb02930.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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