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PubMed2003

Partial duplication of the APBA2 gene in chromosome 15q13 corresponds to duplicon structures.

BACKGROUND: Chromosomal abnormalities affecting human chromosome 15q11-q13 underlie multiple genomic disorders caused by deletion, duplication and triplication of intervals in this region. These events are mediated by highly homologous segments of DNA, or duplicons, that facilitate mispairing and unequal cross-over in meiosis. The gene encoding an amyloid precursor protein-binding protein (APBA2) was previously mapped to the distal portion of the interval commonly deleted in Prader-Willi and Angelman syndromes and duplicated in cases of autism. RESULTS: We show that this gene actually maps to a more telomeric location and is partially duplicated within the broader region. Two highly homologous copies of an interval containing a large 5' exon and downstream sequence are located approximately 5 Mb distal to the intact locus. The duplicated copies, containing the first coding exon of APBA2, can be distinguished by single nucleotide sequence differences and are transcriptionally inactive. Adjacent to APBA2 maps a gene termed KIAA0574. The protein encoded by this gene is weakly homologous to a protein termed X123 that in turn maps adjacent to APBA1 on 9q21.12; APBA1 is highly homologous to APBA2 in the C-terminal region and is distinguished from APBA2 by the N-terminal region encoded by this duplicated exon. CONCLUSION: The duplication of APBA2 sequences in this region adds to a complex picture of different low copy repeats present across this region and elsewhere on the chromosome.

Adaptor Proteins, Signal Transducing↗

PubMed1984

[On the hemispheric asymmetry of unilateral spatial neglect].

Many investigators were interested in unilateral spatial neglect (USN) and studied it in various respects. Especially the between-hemispheric difference of USN has been broadly argued. It can be considered as a well accepted fact that there is a difference of frequency of USN between left and right brain-damaged patients, however, there is no consistent opinion whether there are differences of severity and quality. To settle this dispute, 239 right-handed unilateral brain-damaged subjects were investigated on USN. 125 subjects suffered from left hemisphere lesions and 114 from right hemisphere lesions. Two tests; copy of drawings and finger imitation; were performed. On copying of drawings, each patient was required to copy line drawings of cubes, complex two-dimensional geometrical figures and simple two-dimensional geometrical figures. Those who failed to complete either the left- or right-hand side of any one of these drawings were classified as showing USN. Then failures of USN were divided into two different patterns; unilateral omission and unilateral distorsion. Again imitation of various finger patterns was tested with the hand homolateral to lesions. These items were presented by two methods. The subjects saw the dorsal side of the examiner's hand in the first, and palmar side in the second. On the copying of drawings, right brain-damaged subjects had about twice higher incidence of total USN than left brain-damaged subjects. As for omission alone, the incidence with the right hemispheric group was three times as high as the incidence with the left hemispheric group.(ABSTRACT TRUNCATED AT 250 WORDS)

Brain Mapping↗

PubMed2026

The SMN locus in the T2T era: Structure, gene conversion, and clinical implications.

Long-read sequencing, paralog-aware variant calling, and telomere-to-telomere (T2T) human genome assemblies now enable the resolution of copy-, haplotype-, and nucleotide-level complexities in segmentally duplicated loci, which were previously inaccessible with short-read sequencing. In this review, we highlight how current technologies and analysis methods reveal extensive diversity in copy number (CN), structure, and gene conversion within the spinal muscular atrophy-associated survival motor neuron (SMN) locus. We summarize how understanding population-level structural variation could be translated into clinical practice, where a nucleotide-level view of the SMN locus may refine prognostic accuracy beyond SMN2 CN and explain variable treatment responses. Finally, we discuss how the approaches and methodologies required to study the SMN locus may be applied elsewhere, providing a scaffold to characterize other complex human genetic regions.

Humans↗

PubMed1981

Purification and characterization of the membrane adenosine triphosphatase complex from the wild-type and N,N'-dicyclohexylcarbodiimide-resistant strains of Streptococcus faecalis.

We have purified the F1-F0 adenosine triphosphatase complex from wild-type Streptococcus faecalis ATCC 9790 and an N,N'-dicyclohexylcarbodiimide (DCCD)-resistant mutant strain, SF-dcc-8. For preliminary purification of the complex, reconstituted F1-F0, prepared from isolated F1 adenosine triphosphatase and depleted membranes, was extracted with sodium deoxycholate and fractionated by salt precipitation. By means of two-dimensional gel electrophoresis, the F1-F0 complex was purified as a single, catalytically active band in the first dimension and then resolved into constituent subunits under denaturing conditions in the second dimension. The electrophoretic purification of F1-F0 removed a delta-less form of F1 as well as other impurities, including lipoteichoic acid. Both the DCCD-sensitive and the DCCD-resistant F1-F0 adenosine triphosphatase appeared to consist of eight proteins, five of which corresponded to the F1 subunits alpha, beta,, gamma, delta, and epsilon. The F0 sector proteins, designated M27, M15, and M6, had Mr values of 27,000, 15,000, and 6,000, respectively. There appear to be multiple copies of M6 in the complex. [14C]DCCD reacted specifically and covalently with M6 in the wild-type F1-F0 but failed to label the M6 protein in the complex from the DCCD-resistant strain. It is suggested that DCCD resistance in the SF-dcc-8 mutant may be due to a modification of the M6 protein which hinders access of DCCD to the reactive site.

Adenosine Triphosphatases↗

PubMed2001

Recurrent gains and losses of large (84-109 bp) repeats in the rDNA internal transcribed spacer 2 (ITS2) of rhipicephaline ticks.

We studied the internal transcribed spacer 2 (ITS2) in twenty-two spp. of ticks from the subfamily Rhipicephalinae. A 104-109 base pair (bp) region was imperfectly repeated in most ticks studied. Mapping the number of repeat copies on to a phylogeny from the ITS2 showed that there have been many independent gains and losses of repeats. Comparison of the sequences of the repeat copies indicated that in most taxa concerted evolution had played little if any role in the evolution of these regions, as the copies clustered by sequence position rather than species. In our putative secondary structure, each repeat copy can fold into a distinct and almost identical stem-loop complex; a gain or loss of a repeat copy apparently does not impair the function of the ITS2 in these ticks.

Animals↗

PubMed1980

Native ribonucleoprotein is an efficient transcriptional complex of avian myeloblastosis virus.

A native ribonucleoprotein (RNP) complex of avian myeloblastosis virus was prepared under conditions that gave optimal cDNA synthesis. The complex was an autonomous transcriptional unit capable of synthesizing DNA complementary to the RNA virus genome in the absence of exogenous reverse transcriptase (RNA-dependent DNA nucleotidyltransferase), genomic RNA, and primer. The RNA of the RNP complex cannot be translated in an in vitro cell-free translational system. The RNP contains intact viral RNA, the two subunits of the reverse transcriptase (beta and alpha), the p32 polypeptide resulting from the cleavage of the beta subunit into the alpha subunit, and p12. The principal polypeptide constituent of the RNP complex is the highly basic protein p12, which occurs at a molar ratio of 40:1 in relation to the beta subunit of the polymerase. When examined by the electron microscope, the RNP complex appears similar to the beaded structure of chromatin fiber. A significant portion of these molecules are circular, with headlike structures attached. The circular nature of the proviral DNA and the ability of the RNP complex to generate large intact cDNA copies from the natural primer end suggest that the 5' and 3' ends of the viral RNA are in proximity when in the RNP complex.

Avian Leukosis Virus↗

PubMed1991

Co-amplification of L1 line elements with localised low copy repeats in Giemsa dark bands: implications for genome organisation.

A repeat sequence island, located at the A3 Giemsa dark band on the mouse X chromosome and consisting of 50 copies of a localised long complex repeat unit (LCRU), features an unusually high concentration of L1 LINE repeat sequences juxtaposed and inserted within the LCRU. Sequence analysis of three independent genomic clones containing L1 LINE elements juxtaposed with the LCRU demonstrates a common junction sequence at the L1/LCRU boundary, suggesting that the high concentration of L1 LINE sequences in the repeat sequence island has arisen by association of an L1 element with an LCRU followed by amplification. The LCRU target site at this common junction sequence bears no resemblance to the target site of an L1 element inserted within one LCRU, indicating there is no specific preferential target site for L1 integration. We propose that co-amplification of L1 LINE elements with localised low copy repeat families throughout the genome could have a major effect on the chromosomal distribution of L1 LINE elements.

Animals↗

PubMed1994

prrA, a putative response regulator involved in oxygen regulation of photosynthesis gene expression in Rhodobacter sphaeroides.

A new locus, prrA, involved in the regulation of photosynthesis gene expression in response to oxygen, has been identified in Rhodobacter sphaeroides. Inactivation of prrA results in the absence of photosynthetic spectral complexes. The prrA gene product has strong homology to response regulators associated with signal transduction in other prokaryotes. When prrA is present in multiple copies, cells produce light-harvesting complexes under aerobic growth conditions, suggesting that prrA affects photosynthesis gene expression positively in response to oxygen deprivation. Analysis of the expression of puc::lacZ fusions in wild-type and PrrA- cells revealed a substantial decrease in LacZ expression in the absence of prrA under all conditions of growth, especially when cells were grown anaerobically in the dark in the presence of dimethyl sulfoxide. Northern (RNA) and slot blot hybridizations confirmed the beta-galactoside results for puc and revealed additional positive regulation of puf, puhA, and cycA by PrrA. The effect of truncated PrrA on photosynthesis gene expression in the presence of low oxygen levels can be explained by assuming that PrrA may be effective as a multimer. PrrA was found to act on the downstream regulatory sequences (J. K. Lee and S. Kaplan, J. Bacteriol. 174:1146-1157, 1992) of the puc operon regulatory region. Finally, two spontaneous prrA mutations that abolish prrA function by changing amino acids in the amino-terminal domain of the protein were isolated.

Aldehyde Oxidoreductases↗

PubMed1982

Nonadenylylated mRNA is present as polyadenylylated RNA in nuclei of Drosophila.

The sequence complexity of nuclear total RNA and nuclear poly(A)+RNA from Drosophila third-instar larvae was determined by hybridization of these RNAs to labeled single-copy DNA. At saturation, the nuclear poly(A)+ - and total RNA hybridized to 11% and 22.5% of the single-copy DNA, respectively. The increase in complexity of nuclear total RNA over that observed for nuclear poly(A)+RNA indicates the presence of a discrete class of nonoadenylylated nuclear RNA molecules. The relationship between DNA sequences coding for nuclear RNA and mRNA was then determined by hybridization of nuclear total and poly(A)+RNA to DNA enriched for mRNA coding sequences. The results of these studies show that those single-copy DNA sequences that are represented in either the poly(A)+ - or poly(A)- mRNA population are transcribed into RNA molecules that appear in the nuclear poly(A)+RNA population.

Animals↗

PubMed1992

Kdp, a bacterial P-type ATPase whose expression and activity are regulated by turgor pressure.

The Kdp ATPase is a P-type ATPase consisting of three large protein subunits in a complex that probably contains 2 copies of each subunit. A small hydrophobic peptide, encoded in the same operon as the large subunits, may also participate. Kdp has very high affinity for K+ and serves to scavenge this ion when its concentration is low. Kdp responds to turgor pressure at two levels, at the level of activity and of expression. Kdp mediates net uptake when turgor is low, but mediates exchange without net change when turgor is normal. Kdp is expressed only when turgor is low. This control is mediated by a pair of regulatory proteins, members of the class of 'sensor-effector' regulators widely distributed in bacteria. It is suggested that low turgor changes the conformation of the KdpD 'sensor' protein, activating its presumed kinase activity to phosphorylate KdpE, the 'effector' protein, and phospho-KdpE in turn turns on expression of the operon that encodes the Kdp complex.

Adenosine Triphosphatases↗

PubMed1992

Usage of human T-cell receptor V beta, J beta, C beta, and V alpha gene segments is not proportional to gene number.

Certain T-cell receptor (TCR) beta-chain variable (V), joining (J), and constant (C) gene segments, as well as TCR alpha-chain V gene segments, are disproportionally represented in TCR alpha and beta cDNA libraries derived from PHA-stimulated peripheral blood lymphocytes. Sequences of 138 TCR alpha clones and 96 TCR beta clones were determined and of these 128 TCR alpha clones and 88 TCR beta clones were found to contain unique combinations of V, J, and C gene segments or to display diversity in N region nucleotides. The frequency of the V, J, and C genes used in the assembly of unique transcripts was ascertained. Of the 24 reported V beta gene families, 21 were observed among the 88 TCR beta clones including four V beta families (V beta 1, V beta 2, V beta 3, and V beta 4) that were represented in the sample 2 1/2-5 times more frequently than would be expected on the basis of copy number within the gene complex. Seventy-eight percent of the clones were positive for C beta 2 and more than half of the clones (53%) used one of two J beta 2 genes: J beta 2.1 was present in 27 clones and J beta 2.7 in 20 clones. TCR V alpha families were also disproportionately represented in this sample. Twenty-five of 30 V alpha families were observed in the sample of 128 clones including six recently reported V alpha families. Three V alpha families, V alpha 2, V alpha 8, and V alpha 23, accounted for approximately 40% of the TCR alpha clones and were represented at 18%, 9.4%, and 13.3%, respectively. Both V alpha 2 and V alpha 8 gene families contain more than one gene; thus the number of clones observed in these families may, in part, be related to gene number. However, V alpha 23, which appears to be a single-copy gene family, is significantly overrepresented in this sample. Although disproportional usage of V beta genes may be accounted for by superantigen exposure, reasons for disproportional usage of J beta, C beta, and V alpha genes are presently unknown.

Base Sequence↗

PubMed1983

Regulation of light-harvesting chlorophyll-binding protein (LHCP) mRNA accumulation during the cell cycle in Chlamydomonas reinhardi.

Light-harvesting chlorophyll a/b protein (LHCP) synthesis is highly regulated during the cell cycle in light-dark synchronized C. reinhardi cells. LHCPs are a family of cytoplasmically synthesized proteins which are imported into the chloroplast. LHCPs are derived from at least two precursor proteins (32 kd and 30 kd) that are synthesized in vitro and immunoprecipitated by antiserum against chlorophyll-protein complex II proteins. A DNA copy of the mRNA encoding a 32 kd LHCP precursor was cloned from cDNA synthesized from poly(A) RNA obtained from mid-light-phase synchronous cells. Using cloned cDNA (pHS16) as a hybridization probe, we found that a single 1.2 kb RNA complementary to pHS16 accumulates in a wave-like manner during the mid-light phase of the 12 hr light-12 hr dark cycle and correlates with the pattern of chlorophyll synthesis. Light, during the light phase in the light-dark cycle, is required for accumulation of this RNA.

Cell Cycle↗

PubMed2004

Mechanism of the closing-in phenomenon in a figure copying task in Alzheimer's disease patients.

The"closing-in phenomenon"in figure copying tasks refers to a tendency to copy near the target, or to overlap the target to be copied. The mechanisms underlying the closing-in phenomenon have not been fully elucidated. We posit that closing-in may be related to the patients'compensatory strategies to overcome visuospatial dysfunction or visuospatial working memory deficit. Thus, it is expected that as the complexity of the target figure or the distance from the target to the copying space is increased, the magnitude of closing-in will be increased. Thirteen patients with Alzheimer's disease (AD) who demonstrated closing-in on a screening test and 15 healthy controls participated in this study. Each subject copied figures in conditions that varied in terms of figure complexity and distance from the target to the copying space. Neither figure complexity nor distance between the target and copying space affected the degree of closing-in in normal subjects. In contrast, in AD patients, the magnitude of closing-in increased as a function of figure complexity; however closing-in was unchanged by varying the distance from the target to the copying space. Our results suggest that copying near the target figure might be the patients'strategy to compensate for their visuospatial dysfunction or visuospatial working memory deficits.

Aged↗

PubMed2000

2-Oxoacid dehydrogenase multienzyme complexes in the halophilic Archaea? Gene sequences and protein structural predictions.

All Archaea catalyse the conversion of pyruvate to acetyl-CoA via a simple pyruvate oxidoreductase. This is in contrast to the Eukarya and most aerobic bacteria, which use the pyruvate dehydrogenase multienzyme complex [PDHC], consisting of multiple copies of three component enzymes: E1 (pyruvate decarboxylase), E2 (lipoate acetyl-transferase) and E3 (dihydrolipoamide dehydrogenase, DHLipDH). Until now no PDHC activity has been found in the Archaea, although DHLipDH has been discovered in the extremely halophilic Archaea and its gene sequence has been determined. In this paper, the discovery and sequencing of an operon containing the DHLipDH gene in the halophilic archaeon Haloferax volcanii are reported. Upstream of the DHLipDH gene are 3 ORFs which show highest sequence identities with the E1alpha, E1beta and E2 genes of the PDHC from gram-positive organisms. Structural predictions of the proposed protein product of the E2 gene show a domain structure characteristic of the E2 component in PDHCs, and catalytically important residues, including the lysine to which the lipoic acid cofactor is covalently bound, are conserved. Northern analyses indicate the transcription of the whole operon, but no PDHC enzymic activity could be detected in cell extracts. The presence in the E2 gene of an insertion (equivalent to approximately 100 aa) not found in bacterial or eukaryal E2 proteins, might be predicted to prevent multienzyme complex assembly. This is the first detailed report of the genes for a putative 2-oxoacid dehydrogenase complex in the Archaea, and the evolutionary and metabolic consequences of these findings are discussed.

3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)↗

PubMed1995

Localized mitochondrial dysfunction in canine myocardial ischemia.

Effects of myocardial ischemia on mitochondrial enzymes and mitochondrial DNA (mtDNA) were examined using the model of Ameroid constriction of canine cardiac vessels. Endocardium supplied by constricted coronary arteries was found to have significantly lower citrate synthase and complex IV activities compared to values obtained from either epicardium supplied by constricted vessels or endocardium supplied by unconstricted coronary arteries. Neither significant differences in mtDNA copy number nor changes in respiratory complexes I, III and V were detected. These results suggest that highly localized, specific mitochondrial enzyme changes result from chronic myocardial ischemia.

Animals↗

PubMed1990

Structure and regulation of KGD2, the structural gene for yeast dihydrolipoyl transsuccinylase.

Yeast mutants assigned to the pet complementation group G104 were found to lack alpha-ketoglutarate dehydrogenase activity as a result of mutations in the dihydrolipoyl transsuccinylase (KE2) component of the complex. The nuclear gene KGD2, coding for yeast KE2, was cloned by transformation of E250/U6, a G104 mutant, with a yeast genomic library. Analysis of the KGD2 sequence revealed an open reading frame encoding a protein with a molecular weight of 52,375 and 42% identities to the KE2 component of Escherichia coli alpha-ketoglutarate dehydrogenase complex. Disruption of the chromosomal copy of KGD2 in a respiratory-competent haploid yeast strain elicited a growth phenotype similar to that of G104 mutants and abolished the ability to mitochondria to catalyze the reduction of NAD+ by alpha-ketoglutarate. The expression of KGD2 was transcriptionally regulated by glucose. Northern (RNA) analysis of poly(A)+ RNA indicated the existence of two KGD2 transcripts differing in length by 150 nucleotides. The concentrations of both RNAs were at least 10 times lower in glucose (repressed)- than in galactose (derepressed)-grown cells. Different 5'-flanking regions of KGD2 were fused to the lacZ gene of E. coli in episomal plasmids, and the resultant constructs were tested for expression of beta-galactosidase in wild-type yeast cells and in hap2 and hap3 mutants. Results of the lacZ fusion assays indicated that transcription of KGD2 is activated by the HAP2 and HAP3 proteins. The regulated expression of KGD2 was found to depend on sequences that map to a region 244 to 484 nucleotides upstream of the structural gene. This region contains two short sequence elements that differ by one nucleotide from the consensus core (5'-TN[A/G]TTGGT-3') that has been proposed to be essential for binding of the HAP activation complex. These data together with earlier reports on the regulation of the KGD1 and LPD1 genes for the alpha-ketoglutarate and dihydrolipoyl dehydrogenases indicate that all three enzyme components of the complex are catabolite repressed and subject to positive regulation by the HAP2 and HAP3 proteins.

Acyltransferases↗

PubMed2002

Involvement of the HtrA family of proteases in the protection of the cyanobacterium Synechocystis PCC 6803 from light stress and in the repair of photosystem II.

Photosystem II (PSII) is prone to irreversible light-induced damage, with the D1 polypeptide a major target. Repair processes operate in the cell to replace a damaged D1 subunit within the complex with a newly synthesized copy. As yet, the molecular details of PSII repair are relatively obscure despite the critical importance of this process for maintaining PSII activity and cell viability. We are using the cyanobacterium Synechocystis sp. PCC 6803 to identify the various proteases and chaperones involved in D1 turnover in vivo. Two families of proteases are being studied: the FtsH family (four members) of Zn(2+)-activated nucleotide-dependent proteases; and the HtrA (or DegP) family (three members) of serine-type proteases. In this paper, we report the results of our studies on a triple mutant in which all three copies of the htrA gene family have been inactivated. Growth of the mutant on agar plates was inhibited at high light intensities, especially in the presence of glucose. Oxygen evolution measurements indicated that, under conditions of high light, the rate of synthesis of functional PSII was less in the mutant than in the wild-type. Immunoblotting experiments conducted on cells blocked in protein synthesis further indicated that degradation of D1 was slowed in the mutant. Overall, our observations indicate that the HtrA family of proteases are involved in the resistance of Synechocystis 6803 to light stress and play a part, either directly or indirectly, in the repair of PSII in vivo.

Bacterial Proteins↗

PubMed2006

The V-type H+ ATPase: molecular structure and function, physiological roles and regulation.

It was nearly 30 years before the V-type H+ ATPase was admitted to the small circle of bona fide transport ATPases alongside F-type and P-type ATPases. The V-type H+ ATPase is an ATP-driven enzyme that transforms the energy of ATP hydrolysis to electrochemical potential differences of protons across diverse biological membranes via the primary active transport of H+. In turn, the transmembrane electrochemical potential of H+ is used to drive a variety of (i) secondary active transport systems via H+-dependent symporters and antiporters and (ii) channel-mediated transport systems. For example, expression of Cl- channels or transporters next to the V-type H+ ATPase in vacuoles of plants and fungi and in lysosomes of animals brings about the acidification of the endosomal compartment, and the expression of the H+/neurotransmitter antiporter next to the V-type H+ ATPase concentrates neurotransmitters in synaptic vesicles. First found in association with endosomal membranes, the V-type H+ ATPase is now also found in increasing examples of plasma membranes where the proton pump energizes transport across cell membranes and entire epithelia. The molecular details reveal up to 14 protein subunits arranged in (i) a cytoplasmic V1 complex, which mediates the hydrolysis of ATP, and (ii) a membrane-embedded V0 complex, which translocates H+ across the membrane. Clever experiments have revealed the V-type H+ ATPase as a molecular motor akin to F-type ATPases. The hydrolysis of ATP turns a rotor consisting largely of one copy of subunits D and F of the V1 complex and a ring of six or more copies of subunit c of the V0 complex. The rotation of the ring is thought to deliver H+ from the cytoplasmic to the endosomal or extracellular side of the membrane, probably via channels formed by subunit a. The reversible dissociation of V1 and V0 complexes is one mechanism of physiological regulation that appears to be widely conserved from yeast to animal cells. Other mechanisms, such as subunit-subunit interactions or interactions of the V-type H+ ATPase with other proteins that serve physiological regulation, remain to be explored. Some diseases can now be attributed to genetic alterations of specific subunits of the V-type H+ ATPase.

Animals↗