Prevalence of the 281 (Gly→Glu) mutation in hepatoerythropoietic porphyria and porphyria cutanea tarda

Summary The prevalence of the 281 (GlyGlu) mutation in hepatoerythropoietic porphyria (HEP) was investigated by the use of hybridization with a synthetic oligonucleotide probe. The mutation was found in HEP-affected members of two unrelated families from Spain, but was absent in two other patients from Italy and Portugal who also had HEP. Moreover, this mutation was not detected in 13 unrelated cases of familial (type II) porphyria cutanea tarda.     

B → A → B Transitions in a Molecular Dynamics Trajectory of Low Salt DNA Solution

A molecular dynamics simulation of the DNA dodecamer d(CGCATATATGCG) has been performed with AMBER 5.0 under low salt conditions. Both B A and A B transitions are observed. This may have biological significance for the formation of complexes between DNA and TATA-box binding proteins.Supplementary material to this paper is available in electronic form at http://dx.doi.org/10.1007/s0089400060654     

Molecular cloning and expression analysis of three genes encoding starch synthase II in rice

Three starch synthase (SS) genes, OsSSII-1, OsSSII-2 and OsSSII-3, were identified in rice (Oryza sativa L.) and localized to chromosomes 10, 2 and 6, respectively. The three OsSSII full-length cDNAs were cloned, and the predicted amino acid sequences were found to share 52–73% similarity with other members of the plant SSII family. The SS activity of each OsSSII was confirmed by expression and enzyme activity assay in Escherichia coli. Expression profile analysis revealed that OsSSII-1 was expressed in endosperms, leaves and roots; OsSSII-2 was mainly expressed in leaves, while OsSSII-3 was mainly expressed in endosperms. Similar to the OsSSI proteins, the OsSSII-2 and OsSSII-3 proteins were found in the soluble as well as the starch-granule-bound fractions in rice. The roles of the OsSSII proteins in starch biosynthesis in rice and the evolutionary relationships of the genes encoding monocotyledonous and dicotyledonous class-II SS enzymes are discussed.Abbreviations CDS Coding domain sequence - EST Expressed sequence tag - GB Granule-bound - Glc Glucose - SS Starch synthase     

Structural organization of the human eukaryotic initiation factor 5A precursor and its site-directed variant Lys50 → Arg

Summary The molecular properties of the human eukaryotic initiation factor 5A precursor and its site directed Lys50 Arg variant have been investigated and compared. Structure perturbation methods were used to gain information about the protein architecture in solution. Intrinsic and extrinsic spectroscopic probes strategically located in the protein matrix detected the independent unfolding of two molecular regions. Three cystemes out of four were titrated in the native protein and the peculiar presence of a tyrosinate band at neutral pH was detected. At alkaline pH only two tyrosines out of three were titratable in the native protein, with an apparent pK of about 9.9. Native protein and its Lys50 Arg variant reacted in a similar fashion to guanidine and to pH variation, but differently to thermal stress. The complex thermal unfolding of both proteins indicated the presence of intermediates. Spectroscopic data showed that these intermediates are differently structured. Consequently, the two proteins seem to have different unfolding pathways.Abbreviations AEDANS acetyl-N-(8-sulpho-l-naphthyl) ethylene-diamine - CD circular dichroism - DTNB 5,5-dithiobis(2-nitrobenzoic acid) - molar extinction coefficient - molar extinction difference - eIF-5A eukaryotic initiation factor 5A, namely the hypusine-containing protein - eIF-5A precursor [or ec-eIF-5A(Lys)] eukaryotic initiation factor 5A precursor, i.e., the unmodified precursor form of eIF-5A produced inEscherichia coli by expression of human eIF-5AcDNA containing Lys in position 50 - GdnHCI guanidinium chloride - I-AEDANS N-iodo-AEDANS - N-AcCys-AEDANS N-acetylcysteine-AEDANS, Mr, relative molecular mass - ODU optical density unit - RMS root mean square - TrisHCl Tris (hydroxymethyl)amino-methane hydrochloride     

Positional cloning of cDNAs from the human chromosome 3p21–22 region identifies a clustered organization of zinc-finger genes

The human 3p21-22 region is frequently involved in karyotype rearrangements associated with malignancies. The high frequency of allelic loss in this region has been associated with virtually all small cell lung carcinomas and many renal carcinomas. These findings suggest that at least one tumor-suppressor gene might be located in 3p21-22. We have recently reported the isolation of a 750-kb yeast artificial chromosome (YAC) contig from 3p21-22. Here, we describe three new genes isolated from the 3p YAC contig by using a cDNA hybridization selection. Remarkably, the three new genes encode zinc-finger proteins, indicating the presence of a cluster of zinc-finger genes in human chromosome 3p21.     

Pyruvate dehydrogenase (PDH) deficiency caused by a 21-base pair insertion mutation in the Elα subunit

Summary We report the molecular characterization of a case of a functional PDH-El (E1 subunit of pyruvate dehydrogenase) deficiency, a cause of severe congenital lactic acidosis. Residual PDH-El activity was reduced to 10% of normal values, although the subunit appeared to be quantitatively and qualitatively normal at the protein level as determined by Western blotting. The sequence of PDH-El mRNA and the corresponding genomic DNA revealed an in-frame 21-bp insertion between codons 305 and 306 of the normal Ela cDNA. The mutational insert commences with a novel GAT codon and is a nearly perfect tandem duplication of the wild type DNA sequence. A serine phosphorylation site regulating the activity of the PDH complex is altered by this insertion, which in all likelihood is responsible for the functional enzymatic deficiency leading to lactic acidosis.     

A pyoverdine from Pseudomonas putida CFML 90-51 with a Lys ε-amino link in the peptide chain

From Pseudomonas putida CFML 90-51 – a hospital isolate – a pyoverdine was obtained which is characterized by the unusual linkage by the -rather than the -amino group of Lys in the peptide chain. The structure elucidation by spectroscopic methods and degradation reactions is reported.     

Acute intermittent porphyria caused by a C→T mutation that produces a stop codon in the porphobilinogen deaminase gene

Summary A mutation of the porphobilinogen (PBG) deaminase gene that produces the cross-reacting immunological material (CRIM)-negative type of acute intermittent porphyria (AIP) has been identified in one of 43 unrelated patients with this form of the disorder. The mutation is a CT transition that abolishes a PstI recognition site in exon 9 of the gene and converts a codon for glutamine to a stop codon.     

trans activation of the Escherichia coliato structural genes by a regulatory protein from Bacillus megaterium : potential use in polyhydroxyalkanoate production

A Bacillus megaterium genomic fragment, which encoded an activator homologous to σ⁵⁴ regulators and which was capable of activating Escherichia coli ato genes in trans, was detected in a gene library of B.␣megaterium screened for β-ketothiolase activity. The fragment presented only one complete open reading frame (ORF1), which encoded a protein of 398 amino acids. The recombinant plasmid complemented mutations in the Escherichia coli atoC regulatory gene. The constitutive expression of the E. coli ato operon mediated by ORF1 could be useful for the synthesis of polyhydroxyalkanoates with different flexibility properties by recombinant E. coli strains. Received: 20 October 1997 / Received revision: 18 February 1998 / Accepted: 23 February 1998     

Molecular cloning of novel α-gliadin genes from Crithopsis delileana and the evolution analysis with those from Triticeae

The α-gliadins from Crithopsis delileana (Schult) Roshev (2n=2x=14, KK) were investigated by Acid polyacrylamide gel electrophoresis (A-PAGE) analysis. It was indicated that the electrophoresis mobility of gliadins from C.delileana had obvious difference with those from common wheat in α, γ and ω region. Using primers designed from published sequences of α-gliadin genes, three α-gliadin genes were isolated from C. delileana, which were designated as gli-ka1, gli-ka2 and gli-ka3, respectively. Two in-frame stop codons were found in the coding sequences of gli-ka3, indicating that gli-ka3 could be a pseudogene. The gli-ka2 was a gliadin with an odd number of cysteines, resulting from a non-synonymous mutation. This change might lead to the interactive behavior of gli-ka2. Three α-gliadin genes of C. delileana had the similar but not identical primary structures to the corresponding gene sequences from other wheat related species. By the alignment of α-gliadin genes from Triticeae, phylogenetic analysis indicated that three α-gliadin genes of C. delileana clustered together with all α-gliadin genes from Ee genome of Lophopyrum elongatum by an interior paralleled branch.     

Hemoglobin M Iwate is caused by a C→T transition in codon 87 of the human α1-globin gene

Summary DNA restriction, molecular cloning, and sequencing methods have been used to characterize the mutation leading to the methemoglobinemia HbM Iwate. It could be demonstrated that the HbM Iwate defect is caused by a point mutation involving a transition from C to T in the first position of codon 87 of the ₁-globin gene. Furthermore, the HbM Iwate mutation can directly be identified upon RsaI digestion. This direct detection of the mutation on the gene level is of significant advantage for differential diagnostic purposes.     

Molecular characterization of two types of 22 kilodalton α-zein genes in a gene cluster in maize

Summary Five genes of the -zein subfamily four (SF4) are located in a 56 kb genomic region of the maize inbred line W22. Their nucleotide and deduced amino acid sequences have been determined. The sequences define two types of -zein SF4 genes — type 1 (T1) and type 2 (T2). The single T1 -zein SF4 gene codes for an -zein protein with a M_r of about 22 000. This is the first -zein SF4 gene sequenced that contains no early in-frame stop codons in its coding sequence. The four T2 -zein SF4 genes in this cluster contain one or two early in-frame stop codons. In addition, our T1 and T2 genes differ markedly in the base sequences of their distal 5 non-translated flanking regions. The nucleotide and the deduced amino acid sequences of these two types of -zein SF4 genes are similar ( > 90 %) to one another and to all known -zein SF4 genes and cDNAs. Of the known W22 -zein SF4 genes, only one in six does not contain an early in-frame stop codon. If the number of -zein SF4 genes is 15–20, then we estimate that only about 4 of the W22 -zein SF4 genes are without in-frame early stop codons.     

Changing of Val47 to Asp47 or to Lys47 enhances the immunomodulatory activity of the human Interleukin-l peptide 47–55

The 47–55 domain of the maturehumanInterleukin-was predicted to be exposed by our computational analysis and confirmed to be so by comparing with X-ray crystallographic as well as nuclear magnetic resonance (NMR) spectroscopic data. Four peptides representing fully or part of this domain with sequences 47–55, 41–61, 45–61 and 50–66 were synthesized and tested for their ability to modulate in vivo, the humoral immune response of Balb/c mice to Shigella dysenteriae 116 kDa antigen(s). The smallest immunomodulatory peptide amongst them was found to be the nonapeptide 47–55. To ascertain the structure-function relationships of this 47–55 peptide, various mutant peptides were synthesized and tested for IL-1β ₂ like activity in vivo. Change of Val⁴⁷ to Asp⁴⁷ or to Lys⁴⁷ enhanced its immunomodulatory activity significantly while the change of Gly⁴⁹ to Asp⁴⁹ or Glu⁵⁰ to Ile⁵⁰ or Asp⁵⁴ to Ile⁵⁴ had no such effect. The peptides 47–55 and its mutants were first tested for their ability to elicit inflammatory response like PGE₂ synthesis by a sensitive radioimmunoassay. The peptides which did not have any inflammatory activity were then tested for their ability to stimulate antigen primed T-cells in vitro in the presence of sub-optimal concentration of the antigen.     

Common variations in noncoding regions of the human natriuretic peptide receptor A gene have quantitative effects

Genetic susceptibility to common conditions, such as essential hypertension and cardiac hypertrophy, is probably determined by various combinations of small quantitative changes in the expression of many genes. NPR1, coding for natriuretic peptide receptor A (NPRA), is a potential candidate, because NPRA mediates natriuretic, diuretic, and vasorelaxing actions of the nariuretic peptides, and because genetically determined quantitative changes in the expression of this gene affect blood pressure and heart weight in a dose-dependent manner in mice. To determine whether there are common quantitative variants in human NPR1, we have sequenced the entire human NPR1 gene and identified 10 polymorphic sites in its non-coding sequence by using DNA from 34 unrelated human individuals. Five of the sites are single nucleotide polymorphisms; the remaining five are length polymorphisms, including a highly variable complex dinucleotide repeat in intron 19. There are three common haplotypes 5' to this dinucleotide repeat and three 3' to it, but the 5' haplotypes and 3' haplotypes appear to be randomly associated. Transient expression analysis in cultured cells of reporter plasmids with the proximal promoter sequences of NPR1 and its 3' untranslated regions showed that these polymorphisms have functional effects. We conclude that common NPR1 alleles can alter expression of the gene as much as two-fold and could therefore significantly affect genetic risks for essential hypertension and cardiac hypertrophy in humans.     

Homozygosity for a mutation in the lipoprotein lipase gene (Gly139→Ser) causes chylomicronaemia in a boy of Spanish descent

The enzyme lipoprotein lipase (LPL) plays a crucial role in triglyceride metabolism through catalysis of triglyceride-rich chylomicrons and very low density lipoproteins. Primary LPL deficiency manifests with chylomicronaemia and is caused by mutations in the LPL gene. In this paper we report a novel molecular defect (G₆₇₀A) in exon 4 of the LPL gene, resulting in a substitution of serine for glycine at position 139 in the mature protein. We identified homozygosity for this mutation in a boy of Spanish descent. In vitro mutagenesis provided formal proof that this missense mutation completely abolishes LPL function and therefore is the cause of LPL deficiency.     

Identification of a new point mutation in the human xanthine dehydrogenase gene responsible for a case of classical type I xanthinuria

A 60-year-old Japanese man was diagnosed as having hypouricemia at an annual health check-up. The routine laboratory data was not remarkable except that the patient's hypouricemia and plasma levels of xanthine and hypoxanthine were much higher than those of normal subjects. Furthermore, the patient's daily urinary excretion of xanthine and hypoxanthine was markedly increased compared with reference values. The xanthine dehyrogenase activity of the duodenal mucosa was below the limits of detection. Nevertheless, allopurinol was metabolized to oxypurinol in vivo. Based on these findings, a subtype of classical xanthinuria (type I) was diagnosed. The xanthine dehyrogenase protein was detected by Western blotting analysis. Sequencing of the cDNA of the xanthine dehyrogenase obtained from the duodenal mucosa revealed that a point mutation of C to T had occurred in nucleotide 445. This changed codon 149 from CGC (Arg) to TGC (Cys), a finding that has not been previously reported in patients with classical xanthinuria type I.