Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “structural variants”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,027 records · Page 57Linked to original sources
PubMed1997

A drought-stress-inducible histone gene in Arabidopsis thaliana is a member of a distinct class of plant linker histone variants.

We have isolated and characterized a gene, His1-3, encoding a structurally divergent linker histone in Arabidopsis thaliana. Southern and northern hybridization data indicate that A. thaliana expresses three single-copy linker histone genes, each encoding a structurally distinct variant. H1-3 is a considerably smaller protein (167 amino acids with a mass of 19.0 kDa) than any other described linker histone from higher eukaryotes. We examined the expression of His1-3 at the RNA and protein levels and found that it is induced specifically by water stress. In contrast, expression of His1-1, His1-2 and His4 appear unaffected by water stress. Furthermore, the primary structure of the protein possesses distinct characteristics that are shared with another drought-inducible linker histone, H1-D, isolated from Lycopersicon pennellii. Based on structural characteristics of the deduced protein and its inducible expression, we hypothesize that H1-3 and H1-D are linker histone variants that have specialized roles in the structure and function of plant chromatin and therefore they can be considered to be members of a unique subclass of plant histones. Immunoblotting with an antibody produced against a short polypeptide in the conserved domain of this subtype indicates that similar proteins may exist in other plants.

Amino Acid Sequence↗
PubMedDate not supplied

Structure and variation within variant surface glycoproteins of Trypanosoma brucei.

Variant surface glycoproteins of the African trypanosomes are members of a multigene family which show extraordinary amino sequence diversity. The extent of this diversity and the significance of homologies both in the amino acid sequence and in the post-translational modifications are discussed in the light of what is predicted for the structure of these molecules and what is now known from X-ray crystallographic analysis.

Amino Acid Sequence↗
PubMed2002

Human calcium/calmodulin-dependent protein kinase II gamma gene (CAMK2G): cloning, genomic structure and detection of variants in subjects with type II diabetes.

AIMS/HYPOTHESIS: Ca(2+)/calmodulin-dependent protein kinase II, is expressed in the pancreatic beta cells and is activated by glucose and other secretagogues in a manner correlating with insulin secretion. The activation of Ca(2+)/calmodulin-dependent protein kinase II mediates some of the actions of Ca(2+) on the exocytosis of insulin. We therefore investigated the gene encoding the gamma isoform ( CAMK2G) which has been shown to be expressed in human beta cells as a candidate gene for Type II (non-insulin-dependent) diabetes mellitus. METHODS: Human CAMK2G was cloned from a total human P1 artificial chromosome library using a partial Ca(2+)/calmodulin-dependent protein kinase gamma(E) cDNA probe. Positive PAC clones were localised to chromosome 10q22 by fluorescence in situ hybridisation. To obtain structural information and the sequences of the exon-intron boundaries, the published genomic structures of the rat and mouse genes allowed the putative exon-intron boundaries of human CAMK2G to be amplified by vectorette polymerase chain reaction and sequenced. Sequence variants in each exon were identified using single stranded conformational polymorphism analysis. RESULTS: The human CAMK2G gene comprises 22 exons which range in size between 43 to 230 bp. Screening of the exons and exon-intron boundaries identified two single nucleotide polymorphisms. These did not show association with diabetes in 122 patients and 144 control subjects. CONCLUSIONS/INTERPRETATION: We have identified the genomic structure of CAMK2G to enable further study of this potential candidate gene. Variation in this gene is not strongly associated with diabetes in Caucasians in the United Kingdom. We have identified two single nucleotide polymorphisms which, with appropriately large case control studies, can be used to assess the role of CAMK2G in the susceptibility to Type II diabetes.

Alleles↗
PubMed2001

Human GABA(B)R genomic structure: evidence for splice variants in GABA(B)R1 but not GABA(B)R2.

The type B gamma-aminobutryic acid receptor (GABA(B)R) is a G protein coupled receptor that mediates slow pre- and post-synaptic inhibition in the nervous system. We find that the human GABA(B)R2 gene spans greater than 350 kb and contains 2.8 kb of coding region in 19 exons. The overall similarity in genomic structure with regard to conservation of intron position and exon size between human or Drosophila GABA(B)R1 and GABA(B)R2 genes suggests a common ancestral origin. Multiple transcripts GABA(B)R1a-c and GABA(B)R2a-c have been described and alternative splicing has been proposed to result in GABA(B)R1c, GABA(B)R2b and GABA(B)R2c. The results described here provide support for the existence of GABA(B)R1c but not for GABA(B)R2b and GABA(B)R2c. Splice junctions present in the GABA(B)R1 gene sequence are consistent with the formation of GABA(B)R1c by exon skipping of one sushi domain module. The GABA(B)R2 gene lacks canonical splice junctions for the reported variants. Consistent with this, RNA analysis demonstrates the presence of GABA(B)R1c and GABA(B)R2 transcripts in fetal and adult human brain RNA but GABA(B)R2b and GABA(B)R2c transcripts are not detected. These results provide insight into the evolution and transcript diversity of the mammalian GABA(B)R genes.

Alternative Splicing↗
PubMed1992

Primary structure and alternative splice variants of gephyrin, a putative glycine receptor-tubulin linker protein.

A 93 kd polypeptide associated with the mammalian inhibitory glycine receptor (GlyR) is localized at central synapses and binds with high affinity to polymerized tubulin. This protein, named gephyrin (from the Greek gamma epsilon phi upsilon rho alpha, bridge), is thought to anchor the GlyR to subsynaptic microtubules. Here we report its primary structure deduced from cDNA and show that corresponding transcripts are found in all rat tissues examined. In brain, at least five different gephyrin mRNAs are generated by alternative splicing. Expression of gephyrin cDNAs in 293 kidney cells yields polypeptides reactive with a gephyrin-specific antibody, which coprecipitate with polymerized tubulin. Thus, gephyrin may define a novel type of microtubule-associated protein involved in membrane protein-cytoskeleton interactions.

Amino Acid Sequence↗
PubMed2004

Crystal structure of anticoagulant thrombin variant E217K provides insights into thrombin allostery.

Thrombin is the ultimate protease of the blood clotting cascade and plays a major role in its own regulation. The ability of thrombin to exhibit both pro- and anti-coagulant properties has spawned efforts to turn thrombin into an anticoagulant for therapeutic purposes. This quest culminated in the identification of the E217K variant through scanning and saturation mutagenesis. The antithrombotic properties of E217K thrombin are derived from its inability to convert fibrinogen to a fibrin clot while maintaining its thrombomodulin-dependent ability to activate the anticoagulant protein C pathway. Here we describe the 2.5-A crystal structure of human E217K thrombin, which displays a dramatic restructuring of the geometry of the active site. Of particular interest is the repositioning of Glu-192, which hydrogen bonds to the catalytic Ser-195 and which results in the complete occlusion of the active site and the destruction of the oxyanion hole. Substrate binding pockets are further blocked by residues previously implicated in thrombin allostery. We have concluded that the E217K mutation causes the allosteric inactivation of thrombin by destabilizing the Na(+) binding site and that the structure thus may represent the Na(+)-free, catalytically inert "slow" form.

Allosteric Site↗
PubMed2001

Designed protein G core variants fold to native-like structures: sequence selection by ORBIT tolerates variation in backbone specification.

The solution structures of two computationally designed core variants of the beta 1 domain of streptococcal protein G (G beta 1) were solved by (1)H NMR methods to assess the robustness of amino acid sequence selection by the ORBIT protein design package under changes in protein backbone specification. One variant has mutations at three of 10 core positions and corresponds to minimal perturbations of the native G beta 1 backbone. The other, with mutations at six of 10 positions, was calculated for a backbone in which the separation between G beta 1's alpha-helix and beta-sheet was increased by 15% relative to native G beta 1. Exchange broadening of some resonances and the complete absence of others in spectra of the sixfold mutant bespeak conformational heterogeneity in this protein. The NMR data were sufficiently abundant, however, to generate structures of similar, moderately high quality for both variants. Both proteins adopt backbone structures similar to their target folds. Moreover, the sequence selection algorithm successfully predicted all core chi(1) angles in both variants, five of six chi(2) angles in the threefold mutant and four of seven chi(2) angles in the sixfold mutant. We conclude that ORBIT calculates sequences that fold specifically to a geometry close to the template, even when the template is moderately perturbed relative to a naturally occurring structure. There are apparently limits to the size of acceptable perturbations: In this study, the larger perturbation led to undesired dynamic behavior.

Bacterial Proteins↗
PubMed1989

Prolactin variants in the rat adenohypophysis.

Prolactin (PRL) heterogeneity in the rat pituitary gland was first reported in 1978. Since then, multiple forms of the hormone in the rat pituitary gland have been reported by other investigators. Some of these variants have been ascribed to posttranslational modifications, while the origin of the others is as yet undefined. In this study, the nature, distribution and origin(s) of PRL size variants in the rat adenohypophysis were defined by Western blotting, Northern blot hybridization analysis and pulse-chase approaches. Thirteen structurally related variants, grouped into species with apparent molecular weights (Mr) 97-34,000, 31,000, 24,000 and 22-17,000, were consistently obtained on the basis of their electrophoretic mobilities in nonreducing polyacrylamide gels. Many of the Mr forms were disulphide-linked aggregates. Northern blot analysis suggested that the 24,000 monomeric PRL was encoded by the 0.9 kb mRNA species, while the 45,000 variant could be encoded by the 1.9 kb mRNA. Four PRL variants in the Mr range of 25-46,000 were synthesized concurrently by the mammotrophs in culture. Newly synthesized high Mr variants were also released into the medium and could be detected as early as 1 min after synthesis. Collectively these results suggest that structurally related PRL variants in the rat pituitary gland are due to a combination of posttranscriptional and posttranslational modification of a single gene product. In addition high Mr variants are preferentially secreted over low Mr forms, probably through an alternative secretory pathway.

Animals↗
PubMed1996

Structure of the Val122Ile variant transthyretin - a cardiomyopathic mutant.

The Val122Ile mutant transthyretin (TTR Ile122) is an amyloidogenic protein which has been described as the major protein component of amyloid fibrils isolated from patients with familial amyloidotic cardiomyopathy (FAC), a disease characterized by cardiac failure and amyloid deposits in the heart. The reasons for the deposition of TTR are still unknown and it is conceivable that a conformational alteration, resulting from the mutation, is fundamental for amyloid formation. The three-dimensional structure of TTR Ile122 was determined and refined to a crystallographic R factor of 15.8% at 1.9 A resolution. The r.m.s. deviation from ideality in bond distances is 0.019 A and in angle-bonded distances is 0.027 A. The presence of two crystallographically independent monomers in the asymmetric unit allowed additional means of estimation of atomic coordinate error. The structure of the mutant is essentially identical to that of the wild-type transthyretin (TTR). The largest deviations occur in surface loops and in the region of the substitution. The protein is a tetramer composed of identical subunits; each monomer has two four-stranded beta-sheets which are extended to eight-stranded beta-sheets when two monomers associate through hydrogen bonds forming a dimer, which is the crystallographic asymmetric unit. The replacement of valine for isoleucine introduces very small alterations in relation to the wild-type protein; nevertheless they seem to confirm a tendency for a less stable tetrameric structure. This would support the idea that the tetrameric structure might be disrupted in amyloid fibrils.

Journal Article↗
PubMed1976

Polarization microscopic evidence for an oriented cytoplasmic structure in the "dark" variants of adrenalin-storing cells.

A diffuse cytoplasmic birefringence confined to "dark" adrenalinstoring cells has been described. The main optical characteristics of the birefringence factor include: regular orientation of birefringence relative to the base-apex axis of cells; additive anisotropic staining with methods based on the principle of topo-optical staining reactions; dependence of birefringence on labile morphologic properties. On the basis of the capacity of the macromolecular matrix of chromaffin granules to form lamellar liposomal structures in vitro it has been proposed that a reorientation of molecular organization in the matrix of chromaffin cells is responsible for the observed optical phenomenon. The direction of birefringence was explained by a preferential direction of contractile forces acting during "dark" cell formation.

Adrenal Medulla↗
PubMed2005

Improving immunization of programmable logic controllers using weighted median filters.

This paper addresses the problem of improving immunization of programmable logic controllers (PLC's) to electromagnetic interference with impulsive characteristics. A filtering structure, based on weighted median filters, that does not require additional hardware and can be implemented in legacy PLC's is proposed. The filtering operation is implemented in the binary domain and removes the impulsive noise presented in the discrete input adding thus robustness to PLC's. By modifying the sampling clock structure, two variants of the filter are obtained. Both structures exploit the cyclic nature of the PLC to form an N-sample observation window of the discrete input, hence a status change on it is determined by the filter output taking into account all the N samples avoiding thus that a single impulse affects the PLC functionality. A comparative study, based on a statistical analysis, of the different filters' performances is presented.

Journal Article↗
PubMed2002

On-line post-capillary affinity detection of immunoglobulin G for capillary zone electrophoresis.

To address the quality issues of antibody manufacturing, post-capillary affinity detection of immunoglobulin G (IgG) is developed for capillary zone electrophoresis. In analogy to a two-dimensional separation system, capillary zone electrophoresis (CZE), as the first dimension, resolves IgG variants based on their differences in molecular structure. IgG variants separated by CZE are discriminated against other serum and cellular proteins by affinity complex formation with protein A binding fragment in a post-capillary reactor. The analytical power of post-capillary affinity detection is demonstrated for rapid and selective heterogeneity analysis of human IgG subclasses and monoclonal antibodies in complex sample matrices. By comparing with pre-capillary formation of affinity complexes between IgG and protein A, post-capillary affinity detection clearly exhibit greater resolving power for examining IgG microheterogeneity. Affinity complex formation prior to CZE analysis, however, has the advantage of lower detection limits. Detection limits suffer with post-capillary affinity detection because of the high fluorescence background contributed by the fluorescently labeled protein A in the post-capillary reactor, and the need to determine a small change in the background level upon complex formation.

Electrophoresis, Capillary↗
PubMed1993

X-ray crystal structure of the Ala-109-->Thr variant of human transthyretin which produces euthyroid hyperthyroxinemia.

The structure of the Ala-109-->Thr mutation of human transthyretin, a nonamyloidogenic variant with enhanced thyroxine binding, has been determined by x-ray diffraction to a resolution of 1.7 A. The model, including 175 solvent water molecules, has been refined by constrained least squares to an R-value of 0.157. The standard deviations for protein geometry are 0.016 A for bond distances, 0.5 degree for bond angles, 0.031 A for 1-4 distances, and 0.005 A for deviations of planar groups from their least squares plane. The estimated error in protein atomic coordinates is 0.12 A. Residue 109 extends inward between the two beta sheets which form the major component of the monomer, as does the side chain of residue 30 in the amyloidogenic Met-30 variant. Comparison of the Thr-109 structure with that of the normal shows that the extra atoms of the threonine fit into empty space between sheets and make no extensive changes to the molecular conformation. The substitution at 109 causes small local changes in the secondary structure of the A, G, and H strands resulting in a shift of residues 15-17, 108-110, and 117 in each monomer. The thyroxine-binding sites of the Thr-109 and Met-30 variants and of the normal protein are compared, and the results suggest that the variation in affinity for thyroxine between the three proteins may arise from differences in the size of the binding pocket.

Binding Sites↗
PubMed1992

Alteration in molecular structure which results in disease: the Met-30 variant of human plasma transthyretin.

The structure of a variant transthyretin has been determined by X-ray crystallography at 2.3 A resolution in order to investigate those changes which lead to amyloid formation. This variant transthyretin, in which the internal valyl residue at position 30 is replaced by methionyl, is associated with the most common form of familial amyloidotic polyneuropathy (FAP). Comparison to the known structure of the normal transthyretin tetramer shows that the bulkier methionine residue 30 which lies between the nearly orthogonal beta sheets of the dimer, results in the sheets being displaced an average of 0.4 A. The internal structure of the sheets and of the monomer-monomer interface is maintained. Such global changes may affect the metabolic properties and the tendency towards polymerization of the mutant protein. These findings may form a basis for understanding other amyloid-deposition diseases.

Amino Acid Sequence↗
PubMed2003

Lack of Fas (APO-1/CD95) gene structural alterations or transcript variant ratio changes in breast cancer.

Fas (APO-1/CD95) is a transmembrane receptor protein involved in cell death signaling. Fas receptor and ligand are both expressed in breast cancer cells, however these cells are resistant to apoptosis. Fas gene mutations were detected in hematological and solid tumors, while overexpression of a soluble Fas isoform in serum was related to cancer stage and prognosis. In this work, direct sequencing of exons 6 and 9 of the Fas gene from 90 patients did not reveal any structural alterations. Moreover, no decrease was found in the ratio of the corresponding mRNA species of transmembrane versus soluble Fas isoforms in 31 breast cancer samples compared to 14 controls. Therefore, inhibition of Fas-mediated apoptosis may not be due to structural alterations in the critical exons 6 and 9 of the Fas gene or a shift of expression towards the soluble Fas isoform, but to other mechanisms operating in breast cancer cells.

Apoptosis↗
PubMed2002

Genomic studies of the spleen protein tyrosine kinase locus reveal a complex promoter structure and several genetic variants.

Here we show that the gene of the cytoplasmic tyrosine kinase SYK spans a region of 90kb with 13 coding exons, an alternative exon 14 and at least two 5' untranslated regions exons 1a and 1b. 5' RACE (Rapid amplification of cDNA ends) of human Syk cDNAs demonstrated a complex promoter usage and splicing pattern. We identified three common single nucleotide polymorphisms in the exon la promoter region of the Syk gene as well as a variant Syk cDNA haplotype. This haplotype was characterized by a constellation of 5 silent mutations in the Syk cDNA: 1065(C-T), 1302(G-C), 1338(G-A), 1521(C-T) and 1545(T-C). A hypervariable CATATA(n) repeat polymorphism was also localized to the intron between exons 11 and 12. These novel insights into the genomic organization, promoter structure and genetic variability of Syk will serve as a foundation for detailed molecular epidemiological investigation of its potential role in human cancer biology.

5' Untranslated Regions↗
PubMed2026

Novel bacterial hosts and mobile genetic structure of tet(X) variants in tetracycline-contaminated aquatic environment uncovered by culture and long-read metagenomics.

Clinically important tigecycline (3rd-generation tetracycline) resistance tet(X) variants were inferred to have evolutionarily originated from environmental bacteria, and have been recognized among environment, human and animals. However, genetic basis for environmental proliferation and dissemination of tet(X) variants remains ambiguous. This study profiled tet(X) variants at gene, contig, isolate, and community levels in environmental community subjected to long-term stepwise increasing oxytetracycline (1st-generation tetracycline) or tigecycline pressure using long-term microcosm experiments, quantitative PCR, bacterial isolation, whole-genome sequencing, and Nanopore-based long-read metagenomics. We confirmed that both oxytetracycline and tigecycline enriched the abundance of tetracycline resistance genes especially oxytetracycline-enriched tet(X3). Unexpectedly diverse bacterial hosts and genetic structure of tet(X)-positive mobile elements in the environment microbiome were identified using bacterial isolation and long-read Nanopore metagenomics. Pseudomonas defluvii was first reported to carry tet(X3) in the chromosome, forming IS26-tet(X3)-res-ISCR2 circular intermediate to transfer between different DNA molecules. Database mining revealed similar mobile segments have prevailed among animal-derived Acinetobacter species. Unlike the widely reported ISCR2-mediated transfer of tet(X6), we identified a novel mobile multidrug transposon TnAs3 where tet(X6) and class 1 integron co-transferred as its passenger region. Mobile tet(X2)-ere(D)-aadS-erm(F)-blaOXA-347 segment was annotated in Runella, and co-occurrences of tet(X2) and ere(D), aadS, blaOXA-347 were also found in Flavobacterium, Arsenicibacter, Chryseobacterium and Pedobacter. Overall, tetracycline-contaminated aquatic microbiome harboured diverse mobile tet(X)-positive segments which have not yet been acquired by clinical pathogens, and thus served as the genetic pool of tet(X) variants together with indigenous bacterial hosts, especially the newly reported Pseudomonas defluvii. Reducing pollution of older-generation tetracyclines would be a proactive way to mitigate environmental evolution and possible clinical effects of tet(X) variants.

Metagenomics↗