Translational Elements Research Articles

A phylogenetically conserved hairpin-type 3' untranslated region pseudoknot functions in coronavirus RNA replication.

Secondary and tertiary structures in the 3' untranslated region (UTR) of plus-strand RNA viruses have been postulated to function as control elements in RNA replication, transcription, and translation. Here we describe a 54-nucleotide (nt) hairpin-type pseudoknot within the 288-nt 3' UTR of the bovine coronavirus genome and show by mutational analysis of both stems that the pseudoknotted structure is required for the replication of a defective interfering RNA genome. The pseudoknot is phylogenetically conserved among coronaviruses both in location and in shape but only partially in nucleotide sequence, and evolutionary covariation of bases to maintain G. U pairings indicates that it functions in the plus strand. RNase probing of synthetic transcripts provided additional evidence of its tertiary structure and also identified the possible existence of two conformational states. These results indicate that the 3' UTR pseudoknot is involved in coronavirus RNA replication and lead us to postulate that it functions as a regulatory control element.

Cytoplasmic proteins interact with a translational control element in the protein-coding region of proopiomelanocortin mRNA.

Previous studies have indicated that proopiomelanocortin (POMC) is translationally regulated. We proposed that the regulatory mechanism involves an interaction between trans-acting protein factors and a cis-acting stem-loop structure in the coding region of POMC mRNA. Functional interactions were tested by examining the translation of mouse POMC mRNA in a rabbit reticulocyte system. Specific binding was demonstrated with ultraviolet-crosslinking and RNA gel mobility shift assays. The evidence presented supports our hypothesis that the translational regulation of POMC gene expression involves recognition of the stem-loop by RNA-binding proteins. Furthermore, POMC stem-loop RNA-binding proteins specifically recognized a predicted stem-loop found in the coding region of corticotropin-releasing hormone, suggesting a novel mechanism of gene regulation that may extend to other neuropeptides as well.

Identification of TIAR as a Protein Binding to the Translational Regulatory AU-rich Element of Tumor Necrosis Factor α mRNA

In monocyte/macrophages, the translation of tumor necrosis factor alpha (TNF-alpha) mRNA is tightly regulated. In unstimulated cells, translation of TNF-alpha mRNA is blocked. Upon stimulation with lipopolysaccharides, this repression is overcome, and the mRNA becomes efficiently translated. The key element in this regulation is the AU-rich element (ARE). We have previously reported the binding of two cytosolic protein complexes to the TNF-alpha mRNA ARE. One of these complexes (complex 1) forms with extracts of both unstimulated and lipopolysaccharide-stimulated macrophages and requires a large fragment of the ARE containing clustered AUUUA pentamers. The other complex (complex 2) is only detected after cell activation, binds to a minimal UUAUUUAUU nonamer, and is composed of a 55-kDa protein. Here, we report the identification of the RNA-binding protein TIAR as a protein involved in complex 1. The RNA sequence bound by TIAR and the cytoplasmic localization of this protein in macrophages argue for an involvement of TIAR in TNF mRNA posttranscriptional regulation.

The clam 3' UTR masking element-binding protein p82 is a member of the CPEB family.

During early development gene expression is controlled principally at the translational level. Oocytes of the surf clam Spisula solidissima contain large stockpiles of maternal mRNAs that are translationally dormant or masked until meiotic maturation. Activation of the oocyte by fertilization leads to translational activation of the abundant cyclin and ribonucleotide reductase mRNAs at a time when they undergo cytoplasmic polyadenylation. In vitro unmasking assays have defined U-rich regions located approximately centrally in the 3' UTRs of these mRNAs as translational masking elements. A clam oocyte protein of 82 kDa, p82, which selectively binds the masking elements, has been proposed to act as a translational repressor. Importantly, mRNA-specific unmasking in vitro occurs in the absence of poly(A) extension. Here we show that clam p82 is related to Xenopus CPEB, an RNA-binding protein that interacts with the U-rich cytoplasmic polyadenylation elements (CPEs) of maternal mRNAs and promotes their polyadenylation. Cloned clam p82/CPEB shows extensive homology to Xenopus CPEB and related polypeptides from mouse, goldfish, Drosophila and Caenorhabditis elegans, particularly in their RNA-binding C-terminal halves. Two short N-terminal islands of sequence, of unknown function, are common to vertebrate CPEBs and clam p82. p82 undergoes rapid phosphorylation either directly or indirectly by cdc2 kinase after fertilization in meiotically maturing clam oocytes, prior to its degradation during the first cell cleavage. Phosphorylation precedes and, according to inhibitor studies, may be required for translational activation of maternal mRNA. These data suggest that clam p82 may be a functional homolog of Xenopus CPEB.

Characterization and Chromosomal Mapping of the Human Gene for SFT, a Stimulator of Fe Transport

Hemochromatosis is the most common genetic disorder known in man and results in progressive tissue deposition of iron leading to cirrhosis of the liver, hepatic carcinoma, congestive heart failure, endocrinopathies, and premature death. SFT (stimulator of Fe transport) is a newly discovered transport protein that facilitates uptake of iron. Recent studies have demonstrated that although SFT expression is reciprocally regulated in response to cellular iron levels, it is aberrantly upregulated in the liver of hemochromatosis patients, indicating that enhanced SFT expression contributes to the etiology of this disease. Here we report the molecular cloning and characterization of the human gene for SFT. FISH analysis maps the SFT gene to human chromosome 10q21. PCR analysis indicates 1000 nucleotides of intervening intron sequence near the 3′ end of the coding region for SFT. Based on DNA sequence analysis of the additional 5′ untranslated region obtained from the genomic clone, SFT lacks known metal-regulated transcriptional or translational control elements. These studies provide the basis for future elucidation of the mechanisms that control SFT expression in order to discover how this regulation is lost in hemochromatosis.

A testis-specifically expressed gene is embedded within a cluster of maternally expressed genes at 89B in Drosophila melanogaster.

Differential screening was used to isolate a genomic clone, lambda89Ba located at 89B that hybridised preferentially with female cDNA. On further investigation, a 3.1-kb subfragment, 89Ba(3.1), was shown to contain a gene with male germline-specific expression (Mst89B) flanked by two genes (Mat89Ba and Mat89Bb) expressed predominantly in the ovaries and embryo of Drosophila melanogaster. Mat89Bb is separated from Mst89B by at most 100 bp; Mst89B and Mat89Ba are convergently transcribed and their 3' untranslated regions (UTRs) overlap by a minimum of 85 bp. Database searches with either the 89Ba(3.1) genomic DNA sequence or conceptual translations of Mst89B or Mat89Bb cDNAs failed to reveal any significant similarities with database entries. Using in situ hybridisation to ovaries, Mat89Ba and Mat89Bb were shown to be expressed in nurse cells at stages nine and ten of oogenesis and exported to the oocyte. In addition, Mat89Bb transcripts were detected in the follicle cells surrounding the oocyte. Mst89B transcripts were present throughout spermatogenesis in germline-derived cells, consistent with northern analysis which showed that they were absent in the offspring of tudor flies that lack a germline. The absence of Mst89B transcripts at the tip of the testis suggested that the somatic cells in this region do not express Mst89B. Two 12-bp sequences were identified in the 5' UTR of Mst89B with a strong similarity to translational control elements (TCEs) originally identified in the CGP gene family. This suggests that TCEs may be present in a wider class of testis transcripts.

VIBRATION TRANSMISSION THROUGH SELF-ALIGNING (SPHERICAL) ROLLING ELEMENT BEARINGS: THEORY AND EXPERIMENT

Interest in vibration control in systems employing rolling element bearings, ranging from rotor systems used in energy conversion/transmission to high-precision, multi-degree-of-freedom optical positioning systems, has focused attention on the modelling of bearing dynamic stiffness properties. While modelling a rolling element bearing either as an ideal boundary condition for a shaft or as a simple translational element may suffice in understanding basic rotor system dynamics, such simple models are inadequate in explaining how vibratory energy may be transmitted from, for example, transverse shaft vibrations to perpendicular, out-of-plane casing vibrations. Recently, researchers have begun to address this issue for conventional single row ball or cylindrical rolling element bearings which exhibit a strong moment–coupling stiffness. The study reported in this article focuses on double row spherical (self-aligning) rolling element bearings where moment stiffnesses are negligible, but translational cross-coupling stiffnesses between axial and radial bearing directions are present. A new theoretical model for the direct and cross-coupling stiffness coefficients of spherical rolling element bearings is developed and partially validated using new experimental techniques. It is shown that the coefficient values are complicated functions dependent on radial and axial preloads. While cross-coupling stiffness coefficients are negligible with simple radialoraxial preloads, under the combined radialplusaxial preload condition, the cross-coupling stiffness coefficient between the axial direction and the direction of the radial preload becomes significant.

A method for quantifying positional change of the condyle on lateral tomograms by means of digital subtraction.

A method is described for quantifying the positional change of the condyle on lateral tomograms of the temporomandibular joint (TMJ) by use of digital subtraction. This method permits rotational and translational changes of condylar reference points for easy measurement. Accuracy was evaluated in vitro using both TMJs of two dry human skulls and in vivo with seven volunteers. The average absolute error of the angle of rotation in vitro was 0.67 degrees. For the anterior-posterior element of translation the average absolute error was 0.07 mm, and for the superior-inferior element of translation it was 0.06 mm. From these results, we could conclude that the method provides clinically acceptable measurement accuracy. To verify the usefulness of the method, a clinical application is presented.

Localization-dependent translation requires a functional interaction between the 5' and 3' ends of oskar mRNA.

The precise restriction of proteins to specific domains within a cell plays an important role in early development and differentiation. An efficient way to localize and concentrate proteins is by localization of mRNA in a translationally repressed state, followed by activation of translation when the mRNA reaches its destination. A central issue is how localized mRNAs are derepressed. In this study we demonstrate that, when oskar mRNA reaches the posterior pole of the Drosophila oocyte, its translation is derepressed by an active process that requires a specific element in the 5' region of the mRNA. We demonstrate that this novel type of element is a translational derepressor element, whose functional interaction with the previously identified repressor region in the oskar 3' UTR is required for activation of oskar mRNA translation at the posterior pole. The derepressor element only functions at the posterior pole, suggesting that a locally restricted interaction between trans-acting factors and the derepressor element may be the link between mRNA localization and translational activation. We also show specific interaction of two proteins with the oskar mRNA 5' region; one of these also recognizes the 3' repressor element. We discuss the possible involvement of these factors as well as known genes in the process of localization-dependent translation.

Dissecting the key recognition features of the MS2 bacteriophage translational repression complex.

The MS2 RNA operator capsid offers an unparalleled opportunity to study sequence-specific protein-protein and RNA-protein interactions in molecular detail. RNA molecules encompassing the minimal translational operator recognition elements can be soaked into crystals of RNA-free coat protein shells, allowing the RNA to access the interior of the capsids and make contact with the operator binding sites. Correct interpretation of these structural studies depends critically on functional analysis in solution to confirm that the interactions seen in the crystal are not an artefact of the unusual approach used to generate the RNA-protein complexes. Here we present a series of in vivo and in vitro functional assays, using coat proteins carrying single amino acid substitutions at residues which either interact with the operator RNA or are involved in stabilizing the conformation of the FG loop, the site of the major quasi-equivalent conformational change. Variant operator RNAs have been assayed for coat protein affinity in vitro. The results reveal the robustness of the operator-coat protein interaction and the requirement for both halves of a protein dimer to contact RNA in order to achieve tight binding. They also suggest that there may be a direct link between the conformation of the FG loop and RNA binding.

Post-transcriptional control of Pseudomonas aeruginosa lasB expression involves the 5′ untranslated region of the mRNA

To investigate the regulatory role of the 5′ untranslated region of Pseudomonas aeruginosa lasB mRNA, several lasB-lacZ protein and operon fusions were generated. By examining expression of these fusions in strain PAO1 we showed that the 5′ untranslated leader sequence was involved in the post-transcriptional iron regulation of elastase. Two components of the unusually long 139 nucleotide lasB 5′ untranslated region may be involved in post-transcriptional control. The first 101 nucleotides of the lasB mRNA may contain a translational enhancer element and an element that enhances transcript accumulation. However, the iron responsive element in the lasB mRNA requires sequences downstream of nucleotide +104.

Post-transcriptional control of Pseudomonas aeruginosa lasB expression involves the 5' untranslated region of the mRNA.

To investigate the regulatory role of the 5' untranslated region of Pseudomonas aeruginosa lasB mRNA, several lasB-lacZ protein and operon fusions were generated. By examining expression of these fusions in strain PAO1 we showed that the 5' untranslated leader sequence was involved in the post-transcriptional iron regulation of elastase. Two components of the unusually long 139 nucleotide lasB 5' untranslated region may be involved in post-transcriptional control. The first 101 nucleotides of the lasB mRNA may contain a translational enhancer element and an element that enhances transcript accumulation. However, the iron responsive element in the lasB mRNA requires sequences downstream of nucleotide +104.

Both RNA editing and RNA cleavage are required for translation of tobacco chloroplast ndhD mRNA: a possible regulatory mechanism for the expression of a chloroplast operon consisting of functionally unrelated genes.

Tobacco chloroplast genes encoding a photosystem I component (psaC) and a NADH dehydrogenase subunit (ndhD) are transcribed as a dicistronic pre-mRNA which is then cleaved into short mRNAs. An RNA protection assay revealed that the cleavage occurs at multiple sites in the intercistronic region. There are two possible initiation codons in the tobacco ndhD mRNA: the upstream AUG and the AUG created by RNA editing from the in-frame ACG located 25 nt downstream. Using the chloroplast in vitro translation system, we found that translation begins only from the edited AUG. The extent of ACG to AUG editing is partial and depends on developmental and environmental conditions. In addition, the in vitro assay showed that the psaC/ndhD dicistronic mRNA is not functional and that the intercistronic cleavage is a prerequisite for both ndhD and psaC translation. Using a series of mutant mRNAs, we showed that an intramolecular interaction between an 8 nt sequence in the psaC coding region and its complementary 8 nt sequence in the 5' ndhD UTR is the negative element for translation of the dicistronic mRNA. A possible mechanism in which the differential expression of the chloroplast operon consists of functionally unrelated genes is discussed.

Organisation of regulatory elements in two closely spaced Drosophila genes with common expression characteristics

Sperm tail proteins that are components of a specific structure formed late during spermatid elongation have been found to be encoded by the Mst(3)CGP gene family. These genes have been demonstrated to be regulated both at the transcriptional as well as at the translational level. We report here on the dissection of the regulatory regions for two members of the gene family, Mst84Da and Mst84Db. While high level transcription and negative translational control of Mst84Da is mediated by a short gene segment of 205 nt (−152/+53), Mst84Db expression is controlled by a number of distinct regulatory elements with different effects that all reside within the gene itself. We identify a transcriptional control element between +154 and +216, a translational repression element around +216 to +275 and an RNA stability element within the 3′UTR. Irrespective of the final common expression characteristics, correct regulation for any individual member of the gene family seems to be achieved by very different means. This confirms earlier observations that did not detect any other sequence elements in common apart from the TCE (translational control element).

Separate elements in the 3' untranslated region of the mouse protamine 1 mRNA regulate translational repression and activation during murine spermatogenesis.

The mouse protamine mRNAs, Prm-1 and Prm-2, are translationally repressed for several days during male germ cell differentiation. The translational delay of mouse Prm-1 mRNA has previously been shown to be dependent upon cis-acting elements that reside in the last 62 nucleotides of the Prm-1 3' untranslated region (3' UTR). We have previously identified a 48/50-kDa protein that binds the 3' UTRs of both Prm-1 and Prm-2 mRNAs in a sequence-specific manner, is present in cytoplasmic fractions of postmeiotic round spermatids where the protamine mRNAs are translationally silent, and is markedly reduced in elongated spermatids where the protamine mRNAs become activated for translation. Surprisingly, the binding site for this activity maps to a region of the Prm-1 3' UTR not contained within the functional 62 nucleotides described above. In this report we show that the binding site for the 48/50-kDa protein can also delay translation of a reporter RNA in vivo, suggesting that the 48/50-kDa protein can repress the translation of Prm-1 mRNA during murine spermatogenesis. This observation proves that two separate regions of the Prm-1 3' UTR are sufficient to repress Prm-1 translation. In addition, immunocytochemistry and polysome analysis have revealed that this transgenic reporter mRNA fails to undergo proper translational activation. These results suggest that an additional region of the Prm-1 3' UTR is required for proper translational activation and that Prm-1 translational repression elements can be separated from those involved in translational activation.

Programmed cell death by hok/sok of plasmid R1: Processing at the hok mRNA 3′-end triggers structural rearrangements that allow translation and antisense RNA binding

The hok/sok locus of plasmid R1 mediates plasmid stabilization by killing of plasmid-free cells. The locus specifies two RNAs, hok mRNA and Sok antisense RNA. The post-segregational killing mediated by hok/sok is governed by a complicated control mechanism that involves both post-transcriptional inhibition of translation by Sok-RNA and activation of hok translation by mRNA 3′ processing. Sok-RNA inhibits translation of a reading frame ( mok) that overlaps with hok, and translation of hok is coupled to translation of mok. In the inactive full-length hok mRNA, the translational activator element at the mRNA 5′-end ( tac) is sequestered by the fold-back-inhibitory element located at the mRNA 3′-end ( fbi). The 5′ to 3′ pairing locks the RNA in an inert configuration in which the SD mok and Sok-RNA target regions are sequestered. Here we show that the 3′ processing leads to major structural rearrangements in the mRNA 5′-end. The structure of the refolded RNA explains activation of translation and antisense RNA binding. The refolded RNA contains an antisense RNA target stem-loop that presents the target nucleotides in a single-stranded conformation. The stem of the target hairpin contains SD mok and AUG mok in a paired configuration. Using toeprinting analysis, we show that this pairing keeps SD mok in an accessible configuration. Furthermore, a mutational analysis shows that an internal loop in the target stem is prerequisite for efficient translation and antisense RNA binding.

Coupling of cell division to cell growth by translational control of the G1 cyclin CLN3 in yeast.

The eukaryotic cell cycle is driven by a cascade of cyclins and kinase partners including the G1 cyclin Cln3p in yeast. As the first step in this cascade, Cln3p is uniquely positioned to determine the critical growth-rate threshold for division. To analyze factors regulating CLN3 expression, we identified a short upstream open reading frame (uORF) in the 5' leader of CLN3 mRNA as a translational control element. This control element is critical for the growth-dependent regulation of Cln3p synthesis because it specifically represses CLN3 expression during conditions of diminished protein synthesis or slow growth. Inactivation of the uORF accelerates the completion of Start and entry into the cell cycle suggesting that translational regulation of CLN3 provides a mechanism coupling cell growth and division.

Translation of the chloroplast psbC mRNA is controlled by interactions between its 5' leader and the nuclear loci TBC1 and TBC3 in Chlamydomonas reinhardtii.

Translation of the chloroplast psbC mRNA in Chlamydomonas reinhardtii has been shown previously to require interactions between its 5' untranslated region (5' UTR) and the functions encoded by two nuclear loci, which we name here TBC1 and TBC2. We show that a 97-nucleotide (nt) region located in the middle of the psbC 5' UTR is required for translation initiation. Unlike most procaryotic cis-acting translational control elements, this region has a translational activation function and is located 236 nt upstream from the GUG translation initiation codon. In vivo pulse-labeling of chloroplast-encoded proteins and analyses of the expression of chimeric reporter genes in vivo reveal that a mutation of a newly described locus, TBC3, restores translation from the psbC 5' UTR in the absence of either this cis-acting element or the wild-type trans-acting TBC1 function. These data demonstrate that sequences located in the middle of the psbC 5' UTR, TBC1, and TBC3 functionally interact to control the translation of the psbC mRNA.

Equivalence of pairs of enantiomorphic space groups in the presence ofnon-crystallographic symmetry

The 11 pairs of enantiomorphic space groups with screw axes of opposite handedness generally can be distinguished when the asymmetric unit has known chirality. However, when the asymmetric unit has non-crystallographic rotational symmetry of the same fold or a multiple (in, where i is a positive integer) and the rotation axis is parallel to the screw axis, the screw axis reduces to a pure translational element. Under these circumstances, pairs of enantiomorphic space groups cannot be distinguished.

Molecular characterization of PadA, a phenylacetaldehyde dehydrogenase from Escherichia coli

The padA gene encoding the phenylacetaldehyde dehydrogenase involved in the catabolism of 2-phenylethylamine in Escherichia coli has been cloned, sequenced, and located at 31.0 min on the chromosome. The deduced PadA polypeptide contains 499 amino acid residues with a predicted molecular mass of 53.7 kDa, and its primary structure reveals significant similarity with that of members of the aldehyde dehydrogenase superfamily. By engineering optimal transcription and translation elements, a high expression of the padA gene has been achieved. The active PadA enzyme is a homodimer that prefers NAD + over NADP + as coenzyme. The enzyme efficiently oxidizes only phenylacetaldehyde-like aromatic aldehydes, and has a weak esterase activity with p-nitrophenol. The padA gene constitutes a new catabolic tool for designing DNA cassettes to expand the abilities of microorganisms to degrade toxic aromatic compounds.