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PubMed1995

A novel stress-inducible metallothionein-like gene from rice.

A novel rice genomic sequence encoding coding segments homologous to other metallothionein-like genes was isolated from Oryza sativa genomic library. This sequence, hereby designated as rgMT (rice genomic metallothionein-like gene), consists of two exons and one intron. From the coding sequence, it is predicted that rgMT encodes one protein of 74 amino acids. Differential expression of rgMT in rice plants was observed as mature transcripts were more abundant in roots than in leaves and sheaths. Under different stress conditions, such as excess heavy metals and heat shock, expression of rgMT was significantly elevated. This was especially noticeable with 250 microM CuCl2 for 16 h, 40 degrees C heat for 2 h and 0.06% DMSO for 1 h. Under sucrose starvation, rgMT transcripts also increased with time up to 72 h. During recovery from sucrose starvation, the transcripts declined slightly within 12 h of recovery. rgMT transcripts were also seen to have increased expression in senescent leaves. These results support the notion that rgMT is a stress-inducible gene in rice heretofore unreported.

Abscisic Acid↗

PubMed1988

Organization and structure of Volvox beta-tubulin genes.

Genomic clones encoding two Volvox beta-tubulin genes have been isolated and shown to represent the only two beta-tubulin genes in the genome. Restriction fragment length polymorphism analysis was used to demonstrate that the two genes are genetically linked. One of these genes was sequenced and the mRNA start site(s) determined by primer extension. A comparison of its sequence to those of the two beta-tubulin genes of Chlamydomonas revealed: (1) a high degree of conservation of the coding region, with the predicted amino acid sequence differing only in the C-terminal residue; (2) extensive sequence conservation in the 5' untranslated leader region and a 16 bp (putative regulatory) sequence in the promoter region; (3) the same number and location of introns, with a short region of homology in intron 1, but little significant homology in introns 2 and 3.

Amino Acid Sequence↗

PubMed1975

Deviations from compositional randomness in eukaryotic and prokaryotic proteins: the hypothesis of selective-stochastic stability and a principle of charge conservation.

Eight proteins of diverse lengths, functions, and origin, are examined for compositional non-randomness amino acid by amino acid. The proteins investigated are human fibrinopeptide A, guinea pig Insulin, rattlesnake cytochrome c, MS2 phage coat protein, rabbit triosephosphate isomerase, bovine pancreatic deoxyribonuclease A, bovine glutamate dehydrogenase, and Bacillus thermoproteolyticus thermolysin. As a result of this study the experimentally testable hypothesis is put forth that for a large class of proteins the ratio of that fraction of the molecule which exhibits compositional non-randomness to that fraction which does not is on the average, stable about a mean value (estimated as 0.32 plus or minus 0.17) and (nearly) independent of protein length. Stochastic and selective evolutionary forces are viewed as interacting rather than independent phenomena. With respect to amino acid composition, this coupling ameliorates the current controversy over Darwinian vs. non-Darwinian evolution, selectionist vs. neutralist, in favor of neither: Within the context of the quantitative data, the evolution of real proteins is seen as a compromise between the two viewpoints, both important. The compositional fluctuations of the electrically charged amino acids glutamic and aspartic acid, lysine and arginine, are examined in depth for over eighty protein families, both prokaryotic and eukaryotic. For both taxa, each of the acidic amino acids is present in amounts roughly twice that predicted from the genetic code. The presence of an excess of glutamic acid is independent of the presence of an excess of aspartic acid and vice versa.

Amino Acids↗

PubMed1998

Cloning, nucleotide sequencing, and expression of the 3-methylaspartate ammonia-lyase gene from Citrobacter amalonaticus strain YG-1002.

The gene coding for 3-methylaspartate ammonia-lyase (3-methylaspartase, MAL, EC 4.3.1.2) from Citrobacter amalonaticus strain YG-1002 (TPU 6323) was cloned onto plasmid pBluescript II KS(+), and the nucleotide sequence of the 1239-bp open reading frame (ORF), consisting of 413 codons, was identified as the mal gene coding for MAL. The predicted polypeptide has 62.5% identity with MAL from the obligate anaerobe, Clostridium tetanomorphum NCIMB 11547. ORF1, which showed 58.6% and 58.8% identities with subunit E of the glutamate mutases of C. tetanomorphum and Clostridium cochlearium respectively, was found in the upstream region of the mal gene. An expression plasmid pMALCA3 (5.4 kb), in which the mal gene was expressed under control of the lac promoter on the vector, was constructed. With feeding of 1 mM isopropyl beta-D-thiogalactopyranoside, the amount of the enzyme in a cell-free extract of the transformant, E. coli JM109/pMALCA3, was elevated to 51,800 units/l culture, which is about 50-fold that of C. amalonaticus strain YG-1002. It was calculated that the enzyme comprised over 40% of the total extractable cellular proteins. The enzyme produced by the E. coli transformant was purified in a crystalline form and shown to be identical to that of the wild-type strain with respect to specific activity, molecular mass, subunit structure, enzymological properties, and N-terminal amino acid sequences.

Amino Acid Sequence↗

PubMed2002

Molecular analysis of the Drosophila miniature-dusky ( m-dy) gene complex: m-dy mRNAs encode transmembrane proteins with similarity to C. elegans cuticulin.

Mutations in the Drosophila miniature-dusky ( m-dy) gene complex were first reported by Morgan and Bridges about 90 years ago. m-dy mutants have abnormally small wings, a phenotype attributed to a cell-autonomous reduction in the size of the epidermal cells comprising the differentiated wing. Using a molecular genetic approach, we have characterized the m-dy chromosomal interval and identified a pair of adjacent transcription units corresponding to m and dy. A dy mutant known as dy (And) has a single base substitution within the protein-coding region that is predicted to result in an amber stop codon and premature translational termination. We show that dy mRNA is expressed at two discrete periods during the life cycle--one during embryonic development and early larval instars, the second during adult development, coincident with wing differentiation. In agreement with the phenotypic similarity of m and dy mutants, sequence comparisons reveal a similarity between the predicted MINIATURE and DUSKY proteins, and indicate that the m and dy genes are members of a larger Drosophila gene family. Both m and dy, as well as other members of this superfamily, are predicted to encode transmembrane proteins with similarity to C. elegans cuticle proteins known as cuticulins. We postulate that m, dy and other members of this protein superfamily function as structural components of the Drosophila cuticulin layer. Such a role for m and dy products in wing differentiation is sufficient to explain the morphological phenotypes associated with m-dy mutants.

Amino Acid Sequence↗

PubMed2000

A 5-base insertion in the gammaC-crystallin gene is associated with autosomal dominant variable zonular pulverulent cataract.

A seven-generation family with 30 members affected by highly variable autosomal dominant zonular pulverulent cataracts has been previously described. We have localized the cataracts to a 19-cM interval on chromosome 2q33-q35 including the gamma-crystallin gene cluster. Maximum lod scores are 4.56 (theta=0.02) with D2S157, 3.66 (theta=0.12) with D2S72, and 3.57 (theta=0.052) with CRYG. Sequencing and allele-specific oligonucleotide analysis of the pseudo gammaE-crystallin promoter region from individuals in the pedigree suggest that activation of the gammaE-crystallin pseudo gene is unlikely to cause the cataracts in the family. In addition, base changes in the TATA box but not the Sp1-binding site have been found in unaffected controls and can be excluded as a sole cause of cataracts. In order to investigate the underlying genetic mechanism of cataracts in this family further, exons of the highly expressed gammaC- and gammaD-crystallin genes have been sequenced. The gammaD-crystallin gene shows no abnormalities, but a 5-bp duplication within exon 2 of the gammaC-crystallin gene has been found in one allele of each affected family member and is absent from both unaffected family members and unaffected controls. This mutation disrupts the reading frame of the gammaC-crystallin coding sequence and is predicted to result in the synthesis of an unstable gammaC-crystallin with 38 amino acids of the first "Greek key" motif followed by 52 random amino acids. This finding suggests that the appropriate association of mutant betagamma-crystallins into oligomers is not necessary to cause cataracts and may give us new insights into the genetic mechanism of cataract formation.

Alleles↗

PubMed2026

Pharmacogenomic diversity in Amazonian Indigenous populations: implications for Berlin-Frankfurt-Münster acute lymphoblastic leukemia therapy.

PURPOSE: This study aimed to characterize pharmacogenomic variation in genes involved in the metabolism and transport of drugs used in Berlin-Frankfurt-Münster-based therapy in Amazonian Indigenous individuals and to compare allele frequencies with major continental populations. METHODS/PATIENTS: Whole-exome sequencing data previously generated from 64 healthy Indigenous individuals from 12 Amazonian ethnic groups were analyzed. A total of 120 genes associated with drugs used in Berlin-Frankfurt-Münster protocols were selected. Variants were annotated and filtered using bioinformatic quality-control criteria, and allele frequencies were compared with African, Admixed American, East Asian, European, and South Asian populations from the 1000 Genomes Project. Multidimensional scaling was used to assess population-level genetic similarity. RESULTS: After quality control, 648 variants were identified. Twenty-eight variants were observed exclusively in the Indigenous study population, including four nonsynonymous coding variants with moderate predicted impact. Significant allele-frequency differences were observed for ADA rs11555566, CBR3 rs881711, and CYP2B6 rs3745274; rs881711 and rs3745274 differed from all five reference populations. Multidimensional scaling showed a distinct Indigenous pharmacogenomic profile, with greater similarity to the Admixed American population. CONCLUSIONS: Amazonian Indigenous populations exhibit substantial pharmacogenomic diversity in genes relevant to Berlin-Frankfurt-Münster-based therapy. These findings identify candidate variants for functional and clinical validation and reinforce the importance of including underrepresented populations in pharmacogenomic research.

Acute lymphoblastic leukemia↗

PubMed1984

A new hemoglobin variant altering the alpha 1 beta 2 contact: Hb Chemilly alpha 2 beta 2 99(G1)Asp leads to Val.

Hemoglobin Chemilly (alpha 2 beta 2 99(G1)Asp leads to Val), a high oxygen affinity variant, was uncovered in the red blood cells of a polycythemic patient who reported to the hospital concerning periodic headaches. We describe the molecular abnormality and functional studies of this new abnormal Hb. beta 99(G1)Asp, an invariant residue of hemoglobin, is considered a key amino acid for conformational changes between the R in equilibrium T quaternary structures responsible for the allosteric behavior of hemoglobin. Hb Chemilly exhibits a high O2 affinity, very low cooperativity and reduced Bohr effect. Its functional abnormalities are compared to the 5 other Hb variants at site beta 99(G1) described up to now of the 7 single base substitutions predictable from the genetic code.

Adult↗

PubMed1990

Enzymatic synthesis of dihydrosirohydrochlorin (precorrin-2) and of a novel pyrrocorphin by uroporphyrinogen III methylase.

Uroporphyrinogen III methylase was purified from a recombinant hemB-strain of E. coli harbouring a plasmid containing the cysG gene. N-terminal analysis of this purified protein gave an amino acid sequence corresponding to that predicted from the genetic code. From the u.v./visible spectrum of the reaction catalysed by this SAM dependent methylase it was possible to observe the sequential appearance of the chromophores of a dipyrrocorphin and subsequently of a pyrrocorphin. Confirmation of this transformation was obtained from 13C-NMR studies when it was demonstrated, for the first time directly, that uroporphyrinogen is initially converted into dihydrosirohydrochlorin (precorrin-2) and then, by further methylation, into a novel trimethylpyrrocorphin.

Amino Acid Sequence↗

PubMed1979

Analysis of ECG data, for data compression.

A number of papers on the subject of data reduction techniques applied to ECG Data have recently been published; however, the authors found that most of these articles did not consider quantization techniques, which can be effectively applied to ECG data without any complex parameter extraction procedures. In this paper the authors have looked at the effects of quantization on ECG data and techniques of reducing the amount of data needed to represent these signals. Basically, 3 data reduction techniques, linear prediction using differential pulse code modulation, spectral analysis and slope change detection are investigated and a relative assessment of their performance is presented. This analysis revealed that a slope change detection, as applied to prefiltered data, can be used to represent ECG data at a rate of 2 bits/sample, while maintaining the mean squared error and peak error below 1% and 5% respectively. This technique therefore gives an effective 3 to 1 reduction over the original sampled data, since it was found that the original data could be quantized to 6 bits without significant loss of waveform information.

Electrocardiography↗

PubMed1991

Limited sequence variation in human T-lymphotropic virus type 1 isolates from North American and African patients.

Nucleotide sequences were determined from the env genes of three HTLV-I clones derived from two North American patients and one African patient with adult T-cell leukemia/lymphoma (ATLL). In addition, sequences from the pX region, between env and the 3'LTR, were determined from one of these isolates. These data were compared to sequences derived from HTLV-I isolates of two Japanese ATLL patients, a Japanese patient with HTLV-I-associated myelopathy or tropical spastic paraparesis (HAM/TSP) and a Caribbean ATLL patient. Nucleotide sequence variation was found to be less than 6% in coding and noncoding regions. Predicted amino acid sequences varied between 0.6 and 1.8% in the envelope, 0-3.7% in rex, 0.8-2.5% in the tax gene product, and 3-14.0% in the pX-I open reading frame. Comparisons of the predicted amino acid sequences of the surface envelope protein (SU-gp46) suggest that the variation between isolates of different geographical origins is greater than that between isolates obtained from the same region of the world.

Africa↗

PubMed1993

A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes. The Huntington's Disease Collaborative Research Group.

The Huntington's disease (HD) gene has been mapped in 4p16.3 but has eluded identification. We have used haplotype analysis of linkage disequilibrium to spotlight a small segment of 4p16.3 as the likely location of the defect. A new gene, IT15, isolated using cloned trapped exons from the target area contains a polymorphic trinucleotide repeat that is expanded and unstable on HD chromosomes. A (CAG)n repeat longer than the normal range was observed on HD chromosomes from all 75 disease families examined, comprising a variety of ethnic backgrounds and 4p16.3 haplotypes. The (CAG)n repeat appears to be located within the coding sequence of a predicted approximately 348 kd protein that is widely expressed but unrelated to any known gene. Thus, the HD mutation involves an unstable DNA segment, similar to those described in fragile X syndrome, spino-bulbar muscular atrophy, and myotonic dystrophy, acting in the context of a novel 4p16.3 gene to produce a dominant phenotype.

Amino Acid Sequence↗

PubMed1991

Modification of GP63 genes from diverse species of Leishmania for expression of recombinant protein at high levels in Escherichia coli.

Toward the future development of a defined subunit vaccine against leishmaniasis is, high levels of recombinant GP63 for diverse species of Leishmania were produced in Escherichia coli. Several features of Leishmania GP63 genes were simultaneously modified with the polymerase chain reaction (PCR) using either cloned genes or total genomic DNA from Leishmania as template DNA for the PCR amplification reactions. The PCR products included only the coding region for the predicted mature form of GP63 that occurs on the surface of Leishmania, flanked by the appropriate translation signals and cloning sites for the production of recombinant GP63 as nonfusion protein in E. coli. When the codon usage in the GP63 gene was modified to reduce the guanine and cytosine content for the codons adjacent to the ATG initiation codon, rGP63 represented about 50% of total protein in E. coli. Mouse monoclonal antibodies raised against purified Leishmania major rGP63 had equivalent immunoblotting characteristics for native GP63 and recombinant GP63 with respect to linear determinants on GP63 expressed in diverse species of Leishmania. Human T cell lines and clones were derived from a patient infected with Leishmania braziliensis panamensis using rGP63 purified from an L. major GP63 expression clone as antigen.

Animals↗

PubMed1994

An amplified DNA element in Leishmania encodes potential integral membrane and nucleotide-binding proteins.

LD1 is a 27.5-kb sequence that occurs in an approx. 2.2-Mb chromosome in all species and strains of Leishmania. In Leishmania infantum MHOM/BL/67/ITMAP263, LD1 is also present as an inverted dimeric repeat in multicopy, 55-kb circular molecules. Sequence analysis of a 7873-nt segment derived from the circular DNA reveals 4 open reading frames (ORFs) with potential protein coding function. One ORF predicts a protein with an ATP/GTP binding site motif. Another ORF predicts a protein with 10-12 potential membrane-spanning domains, suggesting that it encodes an integral membrane protein. This protein also has homology with that predicted by the ESAG10 gene of Trypanosoma brucei.

Adenosine Triphosphate↗

PubMed1995

Nucleotide sequence of the Staphylococcus aureus RNA polymerase rpoB gene and comparison of its predicted amino acid sequence with those of other bacteria.

The complete nucleotide sequence of the rpoB gene which encodes the beta subunit of S. aureus RNA polymerase has been determined. The RpoB protein, consists of 1182 amino acids and has a novel initiation codon UUG which initiates protein synthesis with methionine. There is a very strong Shine-Dalgarno complementarity and the -10 and -35 promoter hexameric sequences are TAATAT and CCGTTT, respectively. A rho-dependent termination site, CAATCAA, is present which overlaps the -35 promoter sequence of the adjacent rpoC gene a feature which may have a role in the co-ordinate expression of the two genes. A strong homology and conserved regions were found to exist over the predicted amino acid sequences coding for S. aureus rpoB and the equivalent proteins in Escherichia coli, Pseudomonas putida, Salmonella typhimurium, Chlamydia trachomatis, cyanobacterium Anabaena sp. strain PCC 7120.

Amino Acid Sequence↗

PubMed1989

The complete nucleotide sequence of plum pox potyvirus RNA.

The complete nucleotide sequence of the plum pox virus (PPV) RNA genome has been determined. The RNA sequence is 9786 nucleotides in length, excluding the 3'-terminal poly(A) tail. An AUG triplet at position 147-149 was assigned as the initiation codon for the translation of the genome size viral polyprotein which would consist of 3140 amino acid residues. The nucleotide sequence of the non-coding regions and the predicted amino acid sequence of the polyprotein of PPV were compared with those previously reported for two other potyviruses (tobacco etch virus, TEV, and tobacco vein mottling virus, TVMV), with nucleotide and amino acid sequences of other viruses, as well as with sequences from data banks. The potyvirus genomic expression is discussed in relation to the homologies observed, in particular the predicted protease recognition sequences in related viruses.

Amino Acid Sequence↗

PubMedDate not supplied

A Bacillus subtilis morphogene cluster that includes spoVE is homologous to the mra region of Escherichia coli.

It is known that there is a strong similarity in amino acid sequence between the products of the Escherichia coli morphogenes ftsW (mra region at 2 min) and rodA (mrd region at 14 min) and the Bacillus subtilis SpoVE protein which is required for spore cortex formation. We show here that the predicted amino acid sequences coded for by the genes flanking spoVE are homologous to the products of the E coli genes murD and murG, which flank ftsW, and are involved in peptidoglycan biosynthesis. During vegetative growth and early stationary phase spoVE is cotranscribed with murD and murG in the form of very long polycistronic messages originating upstream of murD. However, this transcriptional activity is shut-off soon (approximately 1 h) after the cells enter stationary phase, and spoVE is then transcribed at two times during sporulation from its own promoter(s). Insertional in vitro mutagenesis of the region revealed that although murD and murG are essential for normal vegetative growth, spoVE is only required for sporulation: spoVE null mutants display a sporulation stage V phenotype indistinguishable by light microscopy from the phenotype conferred by the spoVE85 and spoVE153 alleles that originally defined the locus.

Amino Acid Sequence↗

PubMed1984

Corrected sequences of cDNAs for human salivary and pancreatic alpha-amylases [corrected].

The nucleotide sequences of the cloned human salivary and pancreatic alpha-amylase cDNAs correspond to the continuous mRNA sequences of 1768 and 1566 nucleotides, respectively. These include all of the amino acid coding regions. Salivary cDNA contains 200 bp in the 5'-noncoding region and 32 in the 3'-noncoding region. Pancreatic cDNA contains 3 and 27 bp of 5'- and 3'-noncoding regions, respectively. The nucleotide sequence homology of the two cDNAs is 96% in the coding region, and the predicted amino acid sequences are 94% homologous. Comparison of the sequences of human alpha-amylase cDNAs with those previously obtained for mouse alpha-amylase genes (Hagenbuchle et al., 1980; Schibler et al., 1982) showed the possibility of gene conversion between the two genes of human alpha-amylase.

Amino Acid Sequence↗