Arginine Codon Research Articles

Structure of the Dom34–Hbs1 complex and implications for no-go decay

No-go decay (NGD) targets mRNAs with stalls in translation elongation for endonucleolytic cleavage in a process involving the Dom34 and Hbs1 proteins. The crystal structure of a Schizosaccharomyces pombe Dom34-Hbs1 complex reveals an overall shape similar to that of eRF1-eRF3-GTP and EF-Tu-tRNA-GDPNP. Similarly to eRF1 and GTP binding to eRF3, Dom34 and GTP bind to Hbs1 with strong cooperativity, and Dom34 acts as a GTP-dissociation inhibitor (GDI). A marked conformational change in Dom34 occurs upon binding to Hbs1, leading Dom34 to resemble a portion of a tRNA and to position a conserved basic region in a position expected to be near the peptidyl transferase center. These results support the idea that the Dom34-Hbs1 complex functions to terminate translation and thereby commit mRNAs to NGD. Consistent with this role, NGD at runs of arginine codons, which cause a strong block to elongation, is independent of the Dom34-Hbs1 complex.

Buschke-Ollendorff Syndrome with Striking Phenotypic Variation Resulting from a Novel c.2203C>T Nonsense Mutation in LEMD3

The Buschke-Ollendorff syndrome (BOS) (MIM 166700) is a rare autosomal dominant disorder with highly variable expression that consists of multiple cutaneous elastic nevi and osteopoikilosis. It may exhibit clinical variations, and in some patients either skin or bone lesions may be absent. Recently it has been demonstrated that the heterozygous loss of function in LEMD3 can result in osteopoikilosis, BOS, and melorheostosis. We have studied three generations in a family with BOS with a variable phenotype. The genetic analyses revealed a heterozygous c.2203C>T nonsense mutation at the LEMD3 locus. The mutation induces a change in the 735 arginine codon to a stop codon. This study shows the wide phenotypic variation in BOS and increases the repertory of mutations described to date in LEMD3.

Bioinformatic, structural, and functional analyses support release factor-like MTRF1 as a protein able to decode nonstandard stop codons beginning with adenine in vertebrate mitochondria

Vertebrate mitochondria use stop codons UAA and UAG decoded by the release factor (RF) MTRF1L and two reassigned arginine codons, AGA and AGG. A second highly conserved RF-like factor, MTRF1, which evolved from a gene duplication of an ancestral mitochondrial RF1 and not a RF2, is a good candidate for recognizing the nonstandard codons. MTRF1 differs from other RFs by having insertions in the two external loops important for stop codon recognition (tip of helix alpha5 and recognition loop) and by having key substitutions that are involved in stop codon interactions in eubacterial RF/ribosome structures. These changes may allow recognition of the larger purine base in the first position of AGA/G and, uniquely for RFs, only of G at position 2. In contrast, residues that support A and G recognition in the third position in RF1 are conserved as would be required for recognition of AGA and AGG. Since an assay with vertebrate mitochondrial ribosomes has not been established, we modified Escherichia coli RF1 at the helix alpha5 and recognition loop regions to mimic MTRF1. There was loss of peptidyl-tRNA hydrolysis activity with standard stop codons beginning with U (e.g., UAG), but a gain of activity with codons beginning with A (AAG in particular). A lower level of activity with AGA could be enhanced by solvent modification. These observations imply that MTRF1 has the characteristics to recognize A as the first base of a stop codon as would be required to decode the nonstandard codons AGA and AGG.

Study of Completed Archaeal Genomes and Proteomes: Hypothesis of Strong Mutational AT Pressure Existed in Their Common Predecessor

The number of completely sequenced archaeal genomes has been sufficient for a large-scale bioinformatic study. We have conducted analyses for each coding region from 36 archaeal genomes using the original CGS algorithm by calculating the total GC content (G+C), GC content in first, second and third codon positions as well as in fourfold and twofold degenerated sites from third codon positions, levels of arginine codon usage (Arg2: AGA/G; Arg4: CGX), levels of amino acid usage and the entropy of amino acid content distribution. In archaeal genomes with strong GC pressure, arginine is coded preferably by GC-rich Arg4 codons, whereas in most of archaeal genomes with G+C<0.6, arginine is coded preferably by AT-rich Arg2 codons. In the genome of Haloquadratum walsbyi, which is closely related to GC-rich archaea, GC content has decreased mostly in third codon positions, while Arg4>>Arg2 bias still persists. Proteomes of archaeal species carry characteristic amino acid biases: levels of isoleucine and lysine are elevated, while levels of alanine, histidine, glutamine and cytosine are relatively decreased. Numerous genomic and proteomic biases observed can be explained by the hypothesis of previously existed strong mutational AT pressure in the common predecessor of all archaea.

Hungry Codons Promote Frameshifting in Human Mitochondrial Ribosomes

Human mitochondria are not strict adherents to the universal genetic code, with modifications that include the apparent recoding of two arginine triplets to termination signals. This use of both AGA and AGG occurs rarely in other mammals, and this putative change has long posed a challenging conundrum. A -1 mitoribosome frameshift upstream of the rare codons would necessitate recognition of only the conventional UAA and UAG termination codons. By using a sequence-specific endoribonuclease, we show that the rare arginine codons, presumably in association with other cis elements, promote frameshifting in human mitoribosomes.

Plant mitochondrial RNA editing: The Strasbourg chapter

For 8 years, it was not understood why certain genes of plant mitochondria contain CGG (arginine) codons at positions where tryptophan codons (UGG) are present in the corresponding genes of nonplant species. Identification and sequencing of a tRNA(Trp) gene showed that it is not able to decode the CGG codon. Analysis of different discrepancies in the sequences of plant mitochondrial proteins prompted us to determine directly the corresponding RNA sequences. These experiments showed that plant mitochondrial transcripts are subject to RNA editing that changes C into U, resulting in a better phylogenetic conservation of protein sequences [Gualberto et al. (1989) Nature 341, 660-662].

A Novel GATA1 Mutation (Ter414Arg) in a Family with the Rare X-Linked Blood Group Lu(a-b-) Phenotype.

Abstract 1979Poster Board I-1001The X-borne transcription factor GATA-1 is essential for erythroid and megakaryocyte development. In 1986, Norman et al. (Vox Sang 51:49) described a large family in which the rare Lu(a-b-) blood group phenotype is inherited as the result of an X-borne gene. Serologic and flow cytometric analyses confirmed the suppression of Lutheran blood group antigens on the red blood cells from the original male propositus. Analysis of DNA from the propositus revealed a mutation (1240T>C) in the termination codon of GATA1 converting TGA to a codon for arginine (CGA). The mutation predicts a translated GATA-1 protein containing an additional 41 amino acids at the carboxy terminus. DNA from an unaffected sister of the propositus had a wild-type GATA1 sequence. The GATA1 mutation was not present in 78 random blood donors as determined by restriction fragment length polymorphism (RFLP) analysis using BspHI. The propositus, who is now 64, has an Hb of 122 g/l, a low platelet count (86 × 109/l) with occasional macrothrombocytes (diameter 4-5 um) and a history of bruising easily. Several mutations in the amino terminal zinc finger domain of GATA-1 have been linked with thrombocytopenia and thalassemia or dsyerythropoietic anemia and the presence of macrothrombocytes. Our data provide evidence that mutations outside the zinc finger domain can affect GATA-1 functions in erythroid and megakaryocyte differentiation. In this case, the predicted extended carboxy terminus may interfere with GATA-1 interactions involving other DNA-binding proteins. Disclosures:No relevant conflicts of interest to declare.

Heterologous expression of full-length capsid protein of porcine circovirus 2 in Escherichia coli and its potential use for detection of antibodies

A capsid protein of porcine circovirus 2 (PCV 2) serves as a diagnostic antigen for the detection of PCV 2-associated disease known as a postweaning multisystemic wasting syndrome (PMWS). In this report, a bacterial expression system was developed for the expression and purification of the full-length PCV 2 capsid (Cap) protein from a codon-optimized cap gene. Replacement of rare arginine codons located at the 5′ end of the cap reading frame with codons optimal for E. coli was found to overcome the poor expression of the viral protein in the prokaryotic system. The Cap protein was purified to greater than 95% homogeneity by using a single cation-exchange chromatography at a yield of 10 mg per litre of bacterial culture. Despite the failure of the E. coli-expressed Cap protein to self-assemble into virus-like particles (VLPs), the immunization of mice with recombinant Cap yielded antibodies with the same specificity as those raised against native PCV 2 virions. In addition, the antigenic properties of the purified Cap protein were employed in a subunit-based indirect ELISA to monitor the levels of PCV 2 specific antibodies in piglets originating from a herd which was experiencing PCV 2 infection. These results pave the way for a straightforward large-scale production of the recombinant PCV 2 capsid protein and its use as a diagnostic antigen or a PCV 2 subunit vaccine.

L1CAM mutation in association with X-linked hydrocephalus and Hirschsprung’s disease

X-linked hydrocephalus (XLH) is characterized by increased intracranial ventricle size and head circumference secondary to aqueduct of Sylvius congenital stenosis. Exceedingly rare is the concurrence of XLH and Hirschsprung’s disease (HSCR) with a theoretical incidence of 1 in 125–250 million cases. Herein, we are describing a case of a patient with concurrent XLH and HSCR. The patient was delivered via cesarean section at 37 weeks gestation and underwent uneventful ventriculoperitoneal shunt placement. As a part of a workup for constipation, we performed a rectal biopsy, which was consistent with HSCR. Genetics testing showed hemizygous for R558X hemizygous mutation in the L1CAM gene. A C → T nucleotide substitution in exon 13 resulted in replacement of an arginine codon with a stop codon, a nonsense mutation. Although it is widely accepted that HSCR represents the failure of early embryonic neural crest cells to migrate properly, the exact mechanism is not known. The association of HSCR with XLH in the presence of L1CAM mutations remains quite interesting because cell adhesion molecules are involved in the proper migration of neural components throughout the body. Additional studies are necessary to fully elucidate the relationship between XLH and HSCR in the presence of L1CAM mutations.

Molecular characterization and association with carcass traits of the porcine SLC39A7 gene

In this study, the molecular characterization and potential association of SLC39A7 gene with carcass traits were investigated in pigs. The sequence of SLC39A7 cDNA was obtained by in silico cloning and RT-polymerase chain reaction (PCR). Two transcripts, variant 1 (2398 bp) and variant 2 (2088 bp), of the SLC39A7 gene were identified. Expression analysis of SLC39A7 in 10 different tissues by RT-PCR showed that variant 1 was ubiquitously expressed in all tissues analysed, but variant 2 was not found in fat tissue. The cDNA regions of variant 1 and 2 were organized in seven and eight exons respectively. A c.205G>A substitution in exon 3, which changes a codon for glycine into a codon for arginine, (p.Gly69Arg) and a c.1138-216T>C substitution in intron 6 were detected by PCR-HpaII-restriction fragment length polymorphisms (RFLP) and PCR-cofI-RFLP respectively. Significant differences were found in the allele frequencies of c.205G>A among six Chinese indigenous pig breeds and two commercial pig breeds. Linkage analysis showed that the c.205G>A polymorphism within the SLC39A7 gene was closely linked to the marker Sw1856 on pig chromosome 7 in a Large White x Meishan F(2) resource population. The QTL and association studies between polymorphisms of the SLC39A7 gene and carcass traits were carried out. Significant associations of the SLC39A7 polymorphisms with backfat thickness at thorax-waist (p < 0.05), average backfat thickness (p < 0.05) and leaf fat weight (p < 0.01) were found. Additional F-drop test or marker assisted association analyses also supported the association of the mutation in SLC39A7 with the above traits. Together, the present study provided the useful information for the characterization of SLC39A7 gene and potential association with carcass traits in pigs.

Genotype/phenotype association in von Willebrand disease: is the glass half full or empty?

Since the original description of this disease in 1926, major advances have been made in our understanding of the pathogenetic mechanisms responsible for von Willebrand disease (VWD). We now recognize that this disease comprises a collection of diverse quantitative and qualitative abnormalities of the adhesive protein von Willebrand factor (VWF), the key protein involved in platelet adhesion, and the carrier protein for factor VIII (FVIII) in plasma. Since the mid-1970s there has been a growing appreciation of 'variant' forms of the disease and in the 20 years since the cloning of the VWF gene, much progress has been made in characterizing the molecular genetic pathology of type 3 VWD and the various type 2 variants, types 2A, 2B, 2M and 2N VWD. In all of these cases, mechanistic insights into VWF structure/function have been forthcoming. Most recently, preliminary results relating to the mutational landscape of type 1 disease have been published that highlight the complex pathogenic background of this mild/moderate quantitative trait.

A specific scenario for the origin of life and the genetic code based on peptide/oligonucleotide interdependence.

Among various scenarios that attempt to explain how life arose, the RNA world is currently the most widely accepted scientific hypothesis among biologists. However, the RNA world is logistically implausible and doesn't explain how translation arose and DNA became incorporated into living systems. Here I propose an alternative hypothesis for life's origin based on cooperation between simple nucleic acids, peptides and lipids. Organic matter that accumulated on the prebiotic Earth segregated into phases in the ocean based on density and solubility. Synthesis of complex organic monomers and polymerization reactions occurred within a surface hydrophilic layer and at its aqueous and atmospheric interfaces. Replication of nucleic acids and translation of peptides began at the emulsified interface between hydrophobic and aqueous layers. At the core of the protobiont was a family of short nucleic acids bearing arginine's codon and anticodon that added this amino acid to pre-formed peptides. In turn, the survival and replication of nucleic acid was aided by the peptides. The arginine-enriched peptides served to sequester and transfer phosphate bond energy and acted as cohesive agents, aggregating nucleic acids and keeping them at the interface.

Crystal structure of the E. coli tRNA Arg aminoacyl stem isoacceptor RR-1660 at 2.0 Å resolution

Due to the redundancy of the genetic code there exist six mRNA codons for arginine and several tRNA Arg isoacceptors which translate these triplets to protein within the context of the mRNA. The tRNA identity elements assure the correct aminoacylation of the tRNA with the cognate amino acid by the aminoacyl-tRNA-synthetases. In tRNA Arg, the identity elements consist of the anticodon, parts of the D-loop and the discriminator base. The minor groove of the acceptor stem interacts with the arginyl-tRNA-synthetase. We crystallized different Escherichia coli tRNA Arg acceptor stem helices and solved the structure of the tRNA Arg isoacceptor RR-1660 microhelix by X-ray structure analysis. The acceptor stem helix crystallizes in the space group P1 with the cell constants a = 26.28, b = 28.92, c = 29.00 Å, α = 105.74, β = 99.01, γ = 97.44° and two molecules per asymmetric unit. The RNA hydration pattern consists of 88 bound water molecules. Additionally, one glycerol molecule is bound within the interface of the two RNA molecules.

Transglutaminase-1 gene mutations in autosomal recessive congenital ichthyosis: Summary of mutations (including 23 novel) and modeling of TGase-1

Autosomal recessive congenital ichthyosis (ARCI) is a heterogeneous group of rare cornification diseases. Germline mutations in TGM1 are the most common cause of ARCI in the United States. TGM1 encodes for the TGase-1 enzyme that functions in the formation of the cornified cell envelope. Structurally defective or attenuated cornified cell envelop have been shown in epidermal scales and appendages of ARCI patients with TGM1 mutations. We review the clinical manifestations as well as the molecular genetics of ARCI. In addition, we characterized 115 TGM1 mutations reported in 234 patients from diverse racial and ethnic backgrounds (Caucasion Americans, Norwegians, Swedish, Finnish, German, Swiss, French, Italian, Dutch, Portuguese, Hispanics, Iranian, Tunisian, Moroccan, Egyptian, Afghani, Hungarian, African Americans, Korean, Japanese and South African). We report 23 novel mutations: 71 (62%) missense; 20 (17%) nonsense; 9 (8%) deletion; 8 (7%) splice-site, and 7 (6%) insertion. The c.877-2A>G was the most commonly reported TGM1 mutation accounting for 34% (147 of 435) of all TGM1 mutant alleles reported to date. It had been shown that this mutation is common among North American and Norwegian patients due to a founder effect. Thirty-one percent (36 of 115) of all mutations and 41% (29 of 71) of missense mutations occurred in arginine residues in TGase-1. Forty-nine percent (35 of 71) of missense mutations were within CpG dinucleotides, and 74% (26/35) of these mutations were C>T or G>A transitions. We constructed a model of human TGase-1 and showed that all mutated arginines that reside in the two beta-barrel domains and two (R142 and R143) in the beta-sandwich are located at domain interfaces. In conclusion, this study expands the TGM1 mutation spectrum and summarizes the current knowledge of TGM1 mutations. The high frequency of mutated arginine codons in TGM1 may be due to the deamination of 5' methylated CpG dinucleotides.

Novel transglutaminase-1 mutations and genotype–phenotype investigations of 104 patients with autosomal recessive congenital ichthyosis in the USA

Background:Autosomal recessive congenital ichthyosis (ARCI) is a rare hereditary disorder of cornification. Mutations in the transglutaminase-1 (TGM1) gene, which encodes for the epidermal enzyme transglutaminase-1 (TGase-1), are one of the...

Recombinant Expression of tatABC and tatAC Results in the Formation of Interacting Cytoplasmic TatA Tubes in Escherichia coli

The twin-arginine translocation (Tat) system of bacteria and plant plastids serves to translocate folded proteins across energized biological membranes. In Escherichia coli, the three components TatA, TatB, and TatC mediate this membrane passage. Here we demonstrate that TatA can assemble to form clusters of tube-like structures in vivo. While the presence of TatC is essential for their formation, TatB is not required. The TatA tubes have uniform outer and inner diameters of about 11.5 nm and 6.7 nm, respectively. They align to form a crystalline-like structure in which each tube is surrounded by six TatA tubes. The tube structures become easily detectable even at only a 15-fold overexpression of the tatABC genes. The TatA tubes could also be visualized by fluorescence when untagged TatA was mixed with low amounts of TatA-GFP. The structures were often found in contact with the cell poles. Because TatC is most likely polar in E. coli, as demonstrated by a RR-dependent targeting of translocation-incompatible Tat substrates to the cell poles, and because TatC is required for the formation of aligned TatA tubes, it is proposed that the TatA tubes are initiated at polarly localized TatC.

Sequencing, Genomic Structure, Chromosomal Mapping and Association Study of the Porcine ADAMTS1 Gene with Litter Size

A disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1motif (ADAMTS1) plays a critical role in follicular rupture and represents a major advance in the proteolytic events that control ovulation. In this study, a 9,026-bp DNA sequence containing the full coding region, all 8 introns and part of the 5'and 3' untranslated region of the porcine ADAMTSI gene was obtained. Analysis of the ADAMTSI gene using the porcine radiation hybrid panel indicated that pig ADAMTSI is closely linkage with microsatellite marker S0215, located on SSC13q49. The open reading frame of its cDNA covered 2,844 bp and encoded 947 amino acids. The coding region of porcine ADAMTSI as determined by sequence alignments shared 85% and 81% identity with human and mouse cDNAs, respectively. The deduced protein contained 947 amino acids showing 85% sequence similarity both to the human and mouse proteins, respectively. Comparative sequencing of three pig breeds revealed one single nucleotide polymorphism (SNP) within exon 7 of which a G-C substitution at position 6006 changes a codon for arginine into a codon for proline. The substitution was situated within a PvuII recognition site and developed as a PCR-RFLP marker for further use in population variation investigations and association analysis with litter size. Allele frequencies of this SNP were investigated in seven pig breeds/lines. An association analysis in a new Qingping female line suggested that different ADAMTS1 genotypes have significant differences in litter size (p<0.01).

Mitochondrial RNA editing of F0-ATPase subunit 9 gene (atp9) transcripts of Yunnan purple rice cytoplasmic male sterile line and its maintainer line

On the base of construction of a new type of cytoplasmic male sterile (CMS) line ZidaoA, we analyzed the editing of transcripts of mitochondrial ATP synthase subunit 9 gene (atp9) from CMS line and its maintainer line. With PCR, RT-PCR, and direct sequencing, complete nucleotide sequences were determined for the mitochondrial atp9 gene and its cDNA from two lines of purple rice type rice: CMS line Ying xiang A and its maintainer line Ying xiang B. The atp9 transcript of Ying xiang A was shown to have no editing sites and the transcript of Ying xiang B was shown to have two editing sites with changes affecting the amino acid sequence of the protein product. The editing of the atp9 transcript from Ying xiang B was found to change an arginine codon into a termination codon, shortening the protein of Ying xiang B to the “standard” size. And the Ying xiang A transcript, which has no termination codon, cannot be translated to a normal protein. The results demonstrate the important role of RNA editing in the production of the functional ATP9 subunit and suggest that RNA editing could be likely associated with cytoplasmic male sterility.

Amino Acid Starvation and Colicin D Treatment Induce A-site mRNA Cleavage in Escherichia coli

Escherichia coli possesses a unique RNase activity that cleaves stop codons in the ribosomal aminoacyl-tRNA binding site (A-site) during inefficient translation termination. This A-site mRNA cleavage allows recycling of arrested ribosomes by facilitating recruitment of the tmRNA•SmpB ribosome rescue system. To test whether A-site nuclease activity also cleaves sense codons, we induced ribosome pausing at each of the six arginine codons using three strategies; rare codon usage, arginine starvation, and inactivation of arginine tRNAs with colicin D. In each instance, ribosome pausing induced mRNA cleavage within the target arginine codons, and resulted in tmRNA-mediated SsrA-peptide tagging of the nascent polypeptide. A-site mRNA cleavage did not require the stringent factor ppGpp, or bacterial toxins such as RelE, which mediates a similar nuclease activity. However, the efficiency of A-site cleavage was modulated by the identity of the two codons immediately upstream (5′ side) of the A-site codon. Starvation for histidine and tryptophan also induced A-site cleavage at histidine and tryptophan codons, respectively. Thus, A-site mRNA cleavage is a general response to ribosome pausing, capable of cleaving a variety of sense and stop codons. The induction of A-site cleavage during amino acid starvation suggests this nuclease activity may help to regulate protein synthesis during nutritional stress.

Frameshift events associated with the lysyl-tRNA and the rare arginine codon, AGA, in Escherichia coli: A case study involving the human Relaxin 2 protein

Human Relaxin 2 is an insulin-related peptide hormone with a mass of 19,084 Da. The mRNA contains a number of arginine codons that are rarely used by Escherichia coli to produce highly expressed proteins. As a result, expressing this recombinant protein in E. coli is problematic. When human Relaxin 2 was expressed in E. coli BL21 (DE3), several forms of the protein were made. One species had the expected molecular weight (19,084 Da). A second species observed had a molecular weight of 21,244 Da. A third minor species had a molecular weight of 17,118 Da. These aberrant molecular weights can be explained as follows. First, a sequence CGA-AAA-AAG-AGA, containing the rare arginine codons CGA and AGA was the site of the +1 frameshift that generated the 21,244 Da species. Since there was a limited supply of this arginyl-tRNA, the peptidyl-tRNA moved +1 nucleotide to occupy the codon and resumed protein synthesis. Second, a −1 frameshift associated with ‘slippery A’ sequence XXA-AAA-AAG accounted for 10% of the product with a mass of 17,118 Da. Presumably, the shift to −1 also occurred because there was a paucity of the arginyl-tRNA Arg ucu . Introduction of a plasmid coding for the cognate tRNA for AGA and site directed mutagenesis prevented the formation of both frameshift species.