Synthesis of non-globin proteins in rabbit-erythroid cells. Synthesis of a lipoxygenase in reticulocytes

Primary transcripts: From the discovery of RNA processing to current concepts of gene expression - Review

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.

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

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.

Tissue-specific translational regulation of alternative rabbit 15-lipoxygenase mRNAs differing in their 3'-untranslated regions

By screening a rabbit reticulocyte library, an alternative 15-LOX transcript of 3.6 kb (15-LOX mRNA2) was detected containing a 1019 nt longer 3'-untranslated region (UTR2) than the main 2.6 kb mRNA (15-LOX mRNA1). In anaemic animals, northern blotting showed that 15-LOX mRNA2 was predominantly expressed in non-erythroid tissues, whereas 15-LOX mRNA1 was exclusively expressed in red blood cells and bone marrow. The 15-LOX 3'-UTR2 mRNA2 contained a novel 8-fold repetitive CU-rich motif, 23 nt in length (DICE2). This motif is related but not identical to the 10-fold repetitive differentiation control element (DICE1) of 19 nt residing in the 15-LOX UTR1 mRNA1. DICE1 was shown to interact with human hnRNP proteins E1 and K, thereby inhibiting translation. From tissues expressing the long 15-LOX mRNA2, two to three unidentified polypeptides with molecular weights of 53-55 and 90-93 kDa which bound to DICE2 were isolated by RNA affinity chromatography. A 93 kDa protein from lung cytosol, which was selected by DICE2 binding, was able to suppress translational inhibition of 15-LOX mRNA2, but not of 15-LOX mRNA1, by hnRNP E1. A possible interaction between DICE1/DICE2 cis / trans factors in translational control of 15-LOX synthesis is discussed. Furthermore, the 3'-terminal part of the highly related rabbit leukocyte-type 12-LOX gene was analysed. Very similar repetitive CU-rich elements of the type DICE1 (20 repeats) and DICE2 (nine repeats) were found in the part corresponding to the 3'-UTR of the mRNA.

Regulation of 15-lipoxygenase expression in lung epithelial cells by interleukin-4

We have studied the expression of the 15-lipoxygenase gene in various permanent mammalian cell lines in response to interleukins-4 and -13, and found that none of the cell lines tested expressed 5-, 12- or 15-lipoxygenase when cultured under standard conditions. However, when the lung carcinoma cell line A549 was maintained in the presence of either interleukin for 24 h or more, we observed a major induction of 15-lipoxygenase, as indicated by quantification of 15-lipoxygenase mRNA, by immunohistochemistry, by immunoblot analysis and by enzyme activity assays. This effect was 15-lipoxygenases-specific, since expression of 5- and 12-lipoxygenases remained undetectable. The time course of interleukin-4 treatment indicated maximal accumulation of both 15-lipoxygenase mRNA and functional protein after 48 h. Binding studies revealed that A549 cells express about 2100 high-affinity interleukin-4 binding sites per cell. The interleukin-4 mutant Y124D, which is capable of binding to the interleukin-4 receptor but is unable to trigger receptor activation, counteracted the effect of the wild-type cytokine. Other cell lines, including several epithelial cells and various monocytic cell lines expressing comparable numbers of interleukin-4 receptors, did not express 15-lipoxygenase when stimulated with interleukin-4. These data indicate that A549 cells selectively express 15-lipoxygenase when stimulated with interleukins-4 and -13. The activation of the interleukin-4/13 receptor(s) appears to be mandatory, but not sufficient, for 15-lipoxygenase gene expression.

Calcium promotes membrane association of reticulocyte 15-lipoxygenase

The reticulocyte 15-lipoxygenase (linoleate:oxygen oxidoreductase, EC 1.13.11.12) is implicated in oxidative damage to reticulocyte mitochondria before their elimination by degradation during maturation to the erythrocyte. A proportion of the 15-lipoxygenase sediments with the mitochondrial-rich stromal fraction of density-gradient-fractionated rabbit reticulocytes suggesting a physical association with mitochondria before their elimination. Ca2+ promotes binding of reticulocyte 15-lipoxygenase to isolated rat liver and reticulocyte mitochondria and 15-lipoxygenase-mediated lipid peroxidation of mitochondrial lipids and free linoleic acid. Association of reticulocyte 15-lipoxygenase with isolated mitochondria is not simply a consequence of Ca(2+)-induced swelling, but implies that Ca2+ mediates translocation of soluble lipoxygenase to mitochondrial membranes. Therefore, Ca2+ may have an important physiological role in the regulation of 15-lipoxygenase-mediated targeting of reticulocyte mitochondria for degradation.

Evidence for the appearance of a reticulocyte population low in lipoxygenase mRNA during the recovery from a phenylhydrazine-induced anemia in rabbits

It is shown that during recovery from a phenylhydrazine-induced anemia in rabbits a selective decrease in lipoxygenase mRNA takes place with a corresponding shut-off of the synthesis of the enzyme. It is suggested that a new population, 'recovery'-reticulocytes, makes its appearance in the peripheral blood. Their cells are more mature than the stress macroreticulocytes. A cell-free system prepared from the recovery-reticulocytes exhibits low endogenous synthesis of non-globin polypeptides, even without nuclease treatment, but retains full capacity to be stimulated by exogenous mRNA.

Cloning of a rabbit erythroid-cell-specific lipoxygenase mRNA

We report the isolation of cDNA recombinants representing part of the rabbit reticulocyte (immature red blood cell, RBC) lipoxygenase (LOX) mRNA. One cDNA predicts an amino acid (aa) sequence matching exactly the unique N-terminal 30-aa sequence of the purified enzyme. Further, the reticulocyte mRNA, hybrid-selected by this recombinant, can be translated in vitro to give a polypeptide that comigrates with the purified reticulocyte LOX and is recognized by affinity-purified anti-RBC LOX polyclonal antibodies. Southern blotting experiments hybridising the RBC LOX cDNAs available to total rabbit genomic DNA digested with various restriction enzymes gives a fairly simple hybridisation pattern under moderate stringency conditions: moreover, the same pattern is obtained with a cloned fragment of genomic DNA containing the RBC LOX gene. This indicates that the RBC LOX gene is unique in the genome and seems not to be very closely related to the genes encoding the other tissue LOXs. We also show by Northern transfer/hybridisation experiments that the RBC LOX mRNA is expressed only in the red cell lineage but not in white blood cells (bone marrow or spleen) or in other non-erythroid cells tested (e.g., brain and lung).

Maturation of rabbit reticulocytes: susceptibility of mitochondria to ATP-dependent proteolysis is determined by the maturational state of reticulocyte

A simple procedure is described to separate reticulocytes of different maturity in high yield. It is shown that exhaustion of supply of mitochondria susceptible to degradation by the lipoxygenase-ATP-dependent proteolysis system limits the extent of breakdown of mitochondria during in vitro maturation. The susceptibility of mitochondria depends on the maturity of the reticulocytes. Incubation in the presence of calcium ions and calcium ionophore leads to full susceptibility of mitochondria in immature reticulocytes but has no effect on those in mature reticulocytes which are already fully susceptible to degradation. Conditions which lead to rapid degradation of mitochondria do not affect the behaviour of the reticulocyte count. There appears to be no obligatory connection between the breakdown of mitochondria and of ribosomes.

Molecular analysis of erythropoiesis. A current appraisal

This article considers recent evidence concerning the molecular mechanisms involved in the coordinate regulation of gene expression during red blood cell (RBC) differentiation. Contrary to popular belief, recent evidence shows that only a few of the characteristic RBC proteins are restricted to the erythroid lineage: apart from the globins, an RBC lipoxygenase and (possibly) glycophorin are the only examples for which there is reasonably good evidence. In contrast, the proteins forming the RBC cytoskeleton (spectrin, ankyrin, band 4.1, actin and possibly the major anion exchange transmembrane protein by which the cytoskeleton is attached to the plasma membrane) have closely-related variants in other cell types. Yet two beta-spectrin variants are found exclusively in certain terminally differentiated cells, often only in certain specific regions of the cell membrane. Certain RBC isozymes (e.g. for pyruvate kinase and carbonic anhydrase) and an RBC 19 kD protein (ep19) are also expressed only in a subset of other cell types. This illustrates the importance of gene families which are differentially regulated in certain subsets of cell types during differentiation and development. The expression of the globin genes seems to be regulated mainly at the transcriptional level, although transport of these transcripts to the cytoplasm may be controlled by interactions with other RNAs: stabilisation of globin mRNAs by ribonucleoprotein complexes in the cytoplasm may also be important. In fact, the expression of the globin genes involves two distinct phases: first, structural changes occur in the chromatin surrounding the genes (as determined by sensitivity to digestion by nucleases) and these can be maintained independently of any subsequent transcription. In many cases, these nuclease-sensitive sites in the chromatin correspond to low-level transcription initiation sites and to DNA sequences with regulatory functions when the isolated genes are assayed for transcription in vivo after transfection into cells. How the unlinked alpha- and beta-globin genes are coordinately regulated is not yet understood. Indeed, the alpha- and beta-gene promoters have quite different properties as judged by their responses to DNA replication and to factors known to affect viral gene function (e.g. the cis-acting SV40 enhancer elements and the trans-acting adenovirus regulatory protein, Ela). Other evidence shows that a nuclear protein present only in erythroid cells is able to bind to the beta-globin gene precisely in the region that is hypersensitive to nuclease digestion in chromatin from erythroid cells.(ABSTRACT TRUNCATED AT 400 WORDS)

Mediterranean glucose 6-phosphate dehydrogenase (G6PD) deficiency--near normal decay of the mutant enzyme protein in circulating erythrocytes

Complete removal of leucocytes and platelets from erythrocytes and the development of a sensitized procedure for the assay of G6PD activity allowed the biochemical mechanisms of the Mediterranean variety of G6PD deficiency to be re-evaluated. Activity in the young erythrocytes from 9 G6PD-deficient subjects averaged 0.1% of the levels observed in the corresponding erythrocyte fraction from normal individuals: moreover, the decline of activity during aging of the G6PD-deficient erythrocytes was comparable with that observed for the normal enzyme. Mutant G6PD purified from granulocytes of a G6PD-deficient subject and entrapped within the corresponding erythrocytes was remarkably stable. Exposure of native erythrocytes to an oxidative stress (divicine plus ascorbate) resulted in a decrease of G6PD activity that was significantly more rapid and extensive in control than in G6PD-deficient cells. These results seem to exclude enhanced intracellular breakdown of the mutant protein within the circulating erythrocytes.

Accounting for the ATP-consuming processes in rabbit reticulocytes

The report deals with a detailed balance of ATP production and consumption of the rabbit reticulocyte. The sum-total of ATP produced amounts to 135 mmol . 1-1 . h-1. About 70% of the ATP consumption has been accounted for by specific processes. The main contributing processes are the globin synthesis with about 28%, the Na+, K+-ATPase with 23% and the proteolysis with more than 15%. 30% of ATP consumption has not been accounted for. Cycloheximide (20 microM) leads to a dissociation between synthesis and degradation of proteins, which argues against any obligatory connection between these processes. More than 90% of the lysine liberated from mitochondria by proteolysis were reutilized for the globin synthesis demonstrating the high nitrogen economy of reticulocytes. Each of the ATP-consuming processes studied appears to control ATP production in an independent manner without competition with each other.

Reticulocyte lipoxygenase changes the passive electrical properties of bovine heart submitochondrial particles

Purified reticulocyte lipoxygenase oxygenates the polyunsaturated phospholipids of sonified submitochondrial particles from bovine heart as measured by a burst of oxygen uptake. Over the frequency range of 0.5 to 100 MHz, the complex impedance of the submitochondrial particles as a function of the frequency before and after lipoxygenase attack was measured. From these data, the membrane capacity, the conductivity of the membrane and the conductivity inside the particles were calculated. Lipoxygenase action causes a 4-fold increase in the membrane capacity and a 2-fold increase in the membrane conductivity. Using the method of deformation of electric pulses, kinetic measurements were performed. In parallel to the changes of the passive electric properties, a partial inhibition of NADH oxidase and succinate oxidase was caused by the lipoxygenase attack. Oxygen uptake, changes of the passive electric properties and the inhibition of respiratory enzymes were prevented by lipoxygenase inhibitors. Owing to the high oxygen consumption produced by the lipoxygenase reaction, anaerobiosis was reached within the first 30 s in the closed chamber. Therefore, it must be concluded that the changes in passive electric properties and the inhibition of the respiratory enzymes are due to secondary anaerobic processes such as the hydroperoxidase reaction catalyzed by the lipoxygenase or a slow redistribution of peroxidized membrane lipids. The results are discussed in relation to the breakdown of mitochondria during the maturation process of red cells.

Lipoxygenase mRNA in rabbit reticulocytes. Its isolation, characterization and translational repression

The synthesis of the erythroid lipoxygenase, an enzyme which is of importance for the degradation of mitochondria during the maturation of reticulocytes to erythrocytes, was studied in reticulocytes from bone marrow and in density-separated fractions from peripheral blood of anemic rabbits. Lipoxygenase mRNA was enriched to about 75% by digestion of polysomes with protease K, poly(U)-Sepharose chromatography and repeated sucrose gradient centrifugation. From sucrose gradient centrifugation, electrophoresis and electron microscopy a molecular weight of about 10(6) was calculated. Synthesis of lipoxygenase is absent in erythroblasts, in very young reticulocytes obtained from bone marrow, or in the lightest fractions of reticulocytes from the peripheral blood. More mature blood reticulocytes show a considerable synthesis of the enzyme. The induction of the synthesis of the lipoxygenase seems to be initiated when reticulocytes have reached the peripheral blood. It is shown that lipoxygenase mRNA is present in reticulocytes as a translationally inactive free cytoplasmic messenger ribonucleoprotein (mRNP) particle. After deproteinization isolated mRNA obtained from masked mRNP codes for authentic lipoxygenase in a cell-free protein-synthesizing system of reticulocytes.

Identification of the product formed by human erythrocyte galactosyltransferase

Sepharose 4B-immobilized desialylated ovine submaxillary mucin was used as an acceptor for galactose transfer from UDP-galactose, catalyzed by a Triton X-100-solubilized galactosyltransferase from human erythrocyte ghosts. The product could be cleaved from the insoluble acceptor substrate by alkaline borohydride treatment and identified on Bio-Gel P-2 as a disaccharide. The nature of the glycosidic bond of the isolated material was elucidated by periodate oxidation/NaB[3H]4 reduction/acid hydrolysis and subsequent identification of the aminopolyol formed as L-threosaminitol. Specific cleavage of the enzymatic product by beta-galactosidase indicated a beta-configuration for incorporated galactose. These data permit classification of the enzyme as UDP-galactose: alpha-D-N-acetylgalactosaminyl-protein beta (1 leads to 3) transferase. Furthermore, in the presence of Triton X-100, the enzyme from normal erythrocytes catalyzed transfer of galactose to the glycan moieties of asialo-agalacto-glycophorin in Tn-erythrocytes from a patient with permanent mixed-field polyagglutinability.