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PubMed2002

Structural biology of the C1 complex of complement unveils the mechanisms of its activation and proteolytic activity.

C1 is the multimolecular protease that triggers activation of the classical pathway of complement, a major element of antimicrobial host defense also involved in immune tolerance and various pathologies. This 790,000 Da complex is formed from the association of a recognition protein, C1q, and a catalytic subunit, the Ca2+-dependent tetramer C1s-C1r-C1r-C1s comprising two copies of each of the modular proteases C1r and C1s. Early studies mainly based on biochemical analysis and electron microscopy of C1 and its isolated components have allowed for characterization of their domain structure and led to a low-resolution model of the C1 complex in which the elongated C1s-C1r-C1r-C1s tetramer folds into a more compact, "8-shaped" conformation upon interaction with C1q. A major strategy used over the past years has been to dissect the C1 proteins into modular segments to characterize their function and solve their structure by either X-ray crystallography or nuclear magnetic resonance spectroscopy (NMR). The purpose of this review is to focus on this information, with particular emphasis on the architecture of the C1 complex and the mechanisms underlying its activation and proteolytic activity.

Animals↗

PubMed1997

A novel repeat sequence specific to Mycobacterium tuberculosis complex and its implications.

Restriction fragment length polymorphism analysis of Korean clinical isolates of Mycobacterium tuberculosis using a 245 bp fragment of IS6110 revealed a conserved 3.5 kb Pvull fragment. Attempts to clone this 3.5 kb fragment resulted in the serendipitous discovery of a novel repeat sequence present within a separate 3.5 kb Pvull genomic fragment. Nucleotide sequencing of a 823 bp region containing the putative repeat sequence revealed the presence of three small direct repeats, three palindromes and a 453 bp region that was analogous to 455 bp of a M. tuberculosis sequence previously reported. The presence of this 453 bp repeat sequence was demonstrated in standard mycobacterial strains belonging to the M. tuberculosis complex, including the H37Rv, H37Ra, Erdman, and Canetti strains and M. bovis and M. bovis bacille Calmette-Guérin (BCG). Other mycobacterial species (M. kansasii, M. smegmatis, M. simiae, M. fortuitum, M. scrofulaceum, M. intracellulare, M. avium, and M. haemophilum) did not contain this sequence, suggesting that the 453 bp repeat sequence was specific to the M. tuberculosis complex. Of the 13 Korean and 12 other clinical isolates of M. tuberculosis tested, all contained three to four copies of the repeat sequence. The Southern blot patterns of the various M. tuberculosis strains allowed classification into five different groups. The most frequent pattern was the 'BCG-type' (4.7, 3.5, and 2.4 kb bands); the second most frequent pattern was the '4-band-type' (13, 4.7, 3.5, and 2.4 kb), observed only in the Korean clinical isolates, and the third most common pattern was the M. tuberculosis H37Rv/H37Ra/M. bovis-type (13, 4.7, and 3.5 kb bands). Upstream sequences indicate proximity to the rhamnose biosynthesis (rfb) cluster of M. tuberculosis. Our results indicate that the repeat sequence may be useful for the design of probe and polymerase chain reaction primers for the identification and epidemiological testing of members of the M. tuberculosis complex.

Base Sequence↗

PubMed2000

Breaking the COPI monopoly on Golgi recycling.

The unexpected discovery of a transport pathway from the Golgi to the endoplasmic reticulum (ER) independent of COPI coat proteins sheds light on how Golgi resident enzymes and protein toxins gain access to the ER from as far as the trans Golgi network. This new pathway provides an explanation for how membrane is recycled to allow for an apparent concentration of anterograde cargo at distinct stages of the secretory pathway. As signal-mediated COPI-dependent recycling also involves the concentration of resident proteins into retrograde COPI vesicles, the main bulk of lipids must be recycled, possibly through a COPI-independent pathway.

Coat Protein Complex I↗

PubMed2004

Amplification and overexpression of genes in 17p11.2 ~ p12 in osteosarcoma.

We summarize and briefly discuss recent findings with respect to the amplification and overexpression of candidate oncogenes in 17p11.2 ~p12 in high-grade osteosarcomas. Amplification of this region occurs in about 25% of cases. The amplification profiles are often complex and suggest the involvement of more than one oncogene. The 17p11.2 ~ p12 region harbors many low-copy repeats (LCRs). We propose LCR-mediated repeated duplication by mitotic nonallelic homologous recombination as mechanism for the generation of the amplifications in this region. Genes PMP22 and COPS3 and three expressed sequence tags from within 17p11.2 ~ p12 have been found to be frequently overexpressed and consistently overexpressed after amplification, which identifies them as candidate oncogenes in this region. Overexpression of COPS3 has been linked to TP53 protein degradation and, being equivalent to TP53 mutation, the induction of genomic instability, which frequently occurs in high-grade osteosarcoma. These findings may serve as a framework for future work aimed to identify the causative oncogenes in 17p11.2 ~p12, to clarify the mechanism of their amplification, and to determine their importance in osteosarcoma tumorigenesis.

Bone Neoplasms↗

PubMedDate not supplied

Abnormal craniofacial morphology and cartilage structure in transgenic mice harboring a Gly --> Cys mutation in the cartilage-specific type II collagen gene.

Gross morphology and histology of the craniofacial complex was studied in the offspring of two transgenic founder mice, Gly85-1 and Gly85-3, carrying several copies of a mouse type II collagen transgene that causes a single amino acid substitution (Gly-->Cys) at position 85 of the triple helix. The newborn transgenic mice had a short snout and mandible, a protruding tongue, a cleft of the secondary palate with the tongue situated between the shelves, and a doming cranial vault. Radiological examination revealed that the cranial base of the transgenic mice was shorter and its posterior part downward bent; in addition both the palate and the cribriform plate were less extended in relation to the cranial base than in the controls. Histologically the midline cartilaginous structures were composed of densely packed enlarged chondrocytes in a reduced extracellular matrix containing abnormally thick collagen fibrils. With the exception of the zone of hypertrophic chondrocytes the matrix also showed a loss of glycosaminoglycans. The cellular architecture of the basicranial synchondroses was disorganized, and the nasocerebrally oriented collagen fibrils formed unevenly distributed aggregates. The craniofacial morphology described here for the Gly85 mice shares features typical for other mouse mutations causing short limbed dwarfism. The observations indicate that defective cartilage production causes disproportionate craniofacial growth. Transgenic mice with specific mutations in cartilage-specific genes should therefore be useful for elucidating the complex mechanisms involved in determining the craniofacial growth.

Animals↗

PubMed2006

Template requirements for recognition and copying by Sindbis virus RNA-dependent RNA polymerase.

The Sindbis virus (SIN) nonstructural protein nsP4 possesses the RNA-dependent RNA polymerase activity required for the replication of the SIN genome and transcription of a subgenomic mRNA during infection. Isolation of this protein from other viral components of the RNA synthetic complex allowed the characterization of template requirements for nsP4-mediated genome replication. The major findings of this study are: (i) in the absence of other viral proteins nsP4 is capable of copying SIN plus- and minus-strand templates, but does not transcribe subgenomic RNA; (ii) mutations in the 3' conserved sequence element and poly(A) tail of the plus-strand template prevent nsP4-mediated de novo initiation of minus-strand RNA synthesis; (iii) nsP4-dependent terminal addition of nucleotides occurs on template RNA possessing certain mutations in the 3'CSE and polyadenylate tail ; (iv) nsP4 is capable of minus-strand synthesis independent of the sequence at the 5' end of the template; (v) an A-U rich sequence in the 3'CSE represents a binding site for a replicase component, probably nsP4; (vi) plus-strand genomic RNA synthesis is dependent on the 3' end of the minus-strand template. These studies begin to define the specific interactions with the viral RNA templates mediated by individual components of the viral replication complex and suggest a model for ternary complex formation during the initiation of minus-strand RNA synthesis.

3' Untranslated Regions↗

PubMedDate not supplied

MHC dosage effects on primary immune organ development in the chicken.

Immune development in vertebrates is thought to be influenced by many factors including genotype. We used the Trisomic avian model to probe for influences of the major histocompatibility complex (MHC) on the development of the primary immune organs. Chickens were produced having two, three, and four copies of the MHC-encoding microchromosome. Studies of growth, immune organ development and structure, and lymphocyte populations were performed at three post-hatching time points. Chickens with three and four MHC copies (trisomic and tetrasomic) exhibited reduced overall growth and had smaller bursae and thymuses compared to disomic controls. However, the fold reductions in immune organ weights were much greater than for body weights. Histological analysis of the immune organs revealed dramatic alterations in follicular composition in tetrasomic bursae compared to disomic controls. No obvious alterations were observed in thymic and splenic histology of tetrasomics. Studies of organ lymphocyte numbers revealed a sharp reduction in bursal and thymic lymphocyte counts of trisomic and tetrasomic chickens. Based on these results, it appears that MHC dosage modulates, in a targeted fashion, the cellularity of the primary immune organs through an extended period in differentiation of B and T lymphocytes.

Animals↗

PubMed2001

The crystal structure of an asymmetric complex of the two nucleotide binding components of proton-translocating transhydrogenase.

BACKGROUND: Membrane-bound ion translocators have important functions in biology, but their mechanisms of action are often poorly understood. Transhydrogenase, found in animal mitochondria and bacteria, links the redox reaction between NAD(H) and NADP(H) to proton translocation across a membrane. Linkage is achieved through changes in protein conformation at the nucleotide binding sites. The redox reaction takes place between two protein components located on the membrane surface: dI, which binds NAD(H), and dIII, which binds NADP(H). A third component, dII, provides a proton channel through the membrane. Intact membrane-located transhydrogenase is probably a dimer (two copies each of dI, dII, and dIII). RESULTS: We have solved the high-resolution crystal structure of a dI:dIII complex of transhydrogenase from Rhodospirillum rubrum-the first from a transhydrogenase of any species. It is a heterotrimer, having two polypeptides of dI and one of dIII. The dI polypeptides fold into a dimer. The loop on dIII, which binds the nicotinamide ring of NADP(H), is inserted into the NAD(H) binding cleft of one of the dI polypeptides. The cleft of the other dI is not occupied by a corresponding dIII component. CONCLUSIONS: The redox step in the transhydrogenase reaction is readily visualized; the NC4 atoms of the nicotinamide rings of the bound nucleotides are brought together to facilitate direct hydride transfer with A-B stereochemistry. The asymmetry of the dI:dIII complex suggests that in the intact enzyme there is an alternation of conformation at the catalytic sites associated with changes in nucleotide binding during proton translocation.

Amino Acid Sequence↗

PubMed2000

The 4 A X-ray structure of a tubulin:stathmin-like domain complex.

Phosphoproteins of the stathmin family interact with the alphabeta tubulin heterodimer (tubulin) and hence interfere with microtubule dynamics. The structure of the complex of GDP-tubulin with the stathmin-like domain of the neural protein RB3 reveals a head-to-tail assembly of two tubulins with a 91-residue RB3 alpha helix in which each copy of an internal duplicated sequence interacts with a different tubulin. As a result of the relative orientations adopted by tubulins and by their alpha and beta subunits, the tubulin:RB3 complex forms a curved structure. The RB3 helix thus most likely prevents incorporation of tubulin into microtubules by holding it in an assembly with a curvature very similar to that of the depolymerization products of microtubules.

Amino Acid Sequence↗

PubMed1990

A single base mutation at position 2661 in E. coli 23S ribosomal RNA affects the binding of ternary complex to the ribosome.

A single base substitution mutation from guanine to cytosine was constructed at position 2661 of Escherichia coli 23S rRNA and cloned into the rrnB operon of the multi-copy plasmid pKK3535. The mutant plasmid was transformed into E.coli to determine the effect of the mutation on cell growth as well as the structural and functional properties of the mutant ribosomes in vivo and in vitro. The results show that the mutant ribosomes have a slower elongation rate and an altered affinity for EF-Tu-tRNA-GTP ternary complex. This supports previous findings which indicated that position 2661 is part of a region of 23S rRNA that forms a recognition site for binding of the ternary complex in the ribosomal A site. Combinations of the 2661 mutation with various mutations in ribosomal protein S12 also demonstrate that elements of both ribosomal subunits work in concert to form this binding site.

Cytosine↗

PubMed1995

Chromosome analysis of 97 primary breast carcinomas: identification of eight karyotypic subgroups.

Chromosome banding analysis of 97 short-term cultured primary breast carcinomas revealed clonal aberrations in 79 tumors, whereas 18 were karyotypically normal. In 34 of the 79 tumors with abnormalities, two to eight clones per case were detected; unrelated clones were present in 27 (34%) cases, whereas only related clones were found in seven. These findings indicate that a substantial proportion of breast carcinomas are of polyclonal origin. Altogether eight abnormalities were repeatedly identified both as sole chromosomal anomalies and as part of more complex karyotypes: the structural rearrangements i(1)(q10), der(1:16)(q10;p10), del(1)(q11-12), del(3)(p12-13p14-21), and del(6)(q21-22) and the numerical aberrations +7, +18, and +20. At least one of these changes was found in 41 (52%) of the karyotypically abnormal tumors. They identify a minimum number of cytogenetic subgroups in breast cancer and are likely to represent primary chromosome anomalies in this type of neoplasia. Other candidates for such a role are translocations of 3p12-13 and 4q21 with various partner chromosomes and inversions of chromosome 7, which also were seen repeatedly. Additional chromosomal aberrations that give the impression of occurring nonrandomly in breast carcinomas include structural rearrangements leading to partial monosomies for 1p, 8p, 11p, 11q, 15p, 17p, 19p, and 19q and losses of one copy of chromosomes X, 8, 9, 13, 14, 17, and 22. The latter changes were seen consistently only in complex karyotypes, however, and we therefore interpret them as being secondary anomalies acquired during clonal evolution.

Breast Neoplasms↗

PubMed2000

Increased effect of interferon gamma on PDGF-induced c-fos gene transcription in glomerular mesangial cells: differential effect of the transcriptional coactivator CBP on STAT1alpha activation.

We have previously shown that interferon gamma (IFNgamma) synergistically increases PDGF-induced DNA synthesis in mesangial cells. To examine the mechanism, we studied its effect on PDGF-induced c-fos gene transcription using a reporter mesangial cell in which firefly luciferase gene is driven by c-fos promoter. IFNgamma significantly enhanced PDGF-induced c-fos transcription. We have shown previously that PDGF-induced c-fos transcription in mesangial cells is mediated by the ternary complex factor Elk-1. Using a GAL-4 DNA binding-domain-Elk-1 transactivation domain fusion protein-based reporter assay we showed that the increased effect of IFNgamma was not mediated by Elk-1 transactivation. Gel mobility shift assay of lysates of mesangial cells treated with a combination of IFNgamma and PDGF using sis-inducible DNA element (SIE) showed increased STAT1alpha-SIE complex formation as compared to the PDGF alone. To investigate the transcriptional consequences of this observation, stable reporter mesangial cells in which luciferase gene is driven by four copies of SIE was used. IFNgamma and PDGF in combination significantly increased SIE-dependent transcription as compared to PDGF or IFNgamma alone. Using an antibody in the gel mobility shift assay we showed that the PDGF-induced SIE-STAT1alpha complex recruited the transcriptional coactivator CBP. However, the STAT1alpha-SIE complex formed in the presence of IFNgamma and PDGF did not contain CBP. Taken together, our data provide the first evidence that the synergistic effect of IFNgamma on PDGF-induced DNA synthesis may be the result of increased c-fos gene transcription via SIE. This effect occurs in the presence of increased activation of STAT1alpha without recruitment of the transcriptional coactivator CBP.

Animals↗

PubMed1988

Differences between monkey visual cortex cells in triplet and ghost doublet informational symbols relationships.

On the basis of the recent discovery that precisely replicating triplets of impulses present in All-Interval histograms of spike trains generated by visual cortex cells of Rhesus monkeys are surrounded by multiple copies of "ghost doublets" of such triplets, we have examined and compared in detail, the spike trains generated by four complex cells in the striate cortex of curarized monkeys with respect to: (1) The number of precisely replicating triplet patterns embedded in trains of discharges generated in response to specific Hubel-Wiesel stimulation; (2) The effect of time separating the occurrence of such replicating triplets on the number and time distribution of their ghost doublets; (3) The effect of decreasing the precision criterion for the detection of replicating (parent) triplets (from the standard 0.14 ms criterion to 0.5 ms) on the relationships between triplets and their ghosts and (4) The comparison of the distributions in time of ghost doublets around the first and second copies of triplets when the time intervals separating them were greater than or less than 0.5 s. We found that the precision of replication of triplets varies somewhat from one cell to another, and that ghosts doublets are more copiously associated with replicating triplets emitted near in time to each other than with triplets emitted after larger time intervals, except in the case of one cell. In order to assess the statistical significance of our findings, we systematically shuffled the order of occurrence of intervals in every burst of all the records of one of the studied cells and repeated the analysis. Both the number of replicating triplets and of associated ghost doublets is significantly depressed (but not totally obliterated) by the above shuffling procedure. Finally, further implications based on a model of neural information transmission in the form of temporal correlations between spikes are discussed.

Animals↗

PubMed1983

Molecular basis of length polymorphism in the human zeta-globin gene complex.

The length polymorphism between the human zeta-globin gene and its pseudogene is caused by an allele-specific variation in the copy number of a tandemly repeating 36-base-pair sequence. This sequence is related to a tandemly repeated 14-base-pair sequence in the 5' flanking region of the human insulin gene, which is known to cause length polymorphism, and to a repetitive sequence in intervening sequence (IVS) 1 of the pseudo-zeta-globin gene. Evidence is presented that the latter is also of variable length, probably because of differences in the copy number of the tandem repeat. The homology between the three length polymorphisms may be an indication of the presence of a more widespread group of related sequences in the human genome, which might be useful for generalized linkage studies.

Base Composition↗

PubMed1991

Cryoelectron microscopy of mammalian pyruvate dehydrogenase complex.

Cryoelectron microscopy has been performed on frozen-hydrated pyruvate dehydrogenase complexes from bovine heart and kidney and on various subcomplexes consisting of the dihydrolipoyl transacetylase-based (E2) core and substoichiometric levels of the other two major components, pyruvate dehydrogenase (E1) and dihydrolipoyl dehydrogenase (E3). The diameter of frozen-hydrated pyruvate dehydrogenase complex (PDC) is 50 nm, which is significantly larger than previously reported values. On the basis of micrographs of the subcomplexes, it is concluded that the E1 and E3 are attached to the E2-core complex by extended (4-6 nm maximally) flexible tethers. PDC constructed in this manner would probably collapse and appear smaller than its native size when dehydrated, as was the case in previous electron microscopy studies. The tether linking E1 to the core involves the hinge sequence located between the E1-binding and catalytic domains in the primary sequence of E2, whereas the tether linking E3 is probably derived from a similar hinge-type sequence in component X. Tilting of the E2-based cores and comparison with model structures confirmed that their overall shape is that of a pentagonal dodecahedron. The approximately 6 copies of protein X present in PDC do not appear to be clustered in one or two regions of the complex and are not likely to be symmetrically distributed.

Acetyltransferases↗

PubMed1997

Specific complex formation between the type II bare lymphocyte syndrome-associated transactivators CIITA and RFX5.

Two of the genes defective in the five complementation groups identified in the class II-negative bare lymphocyte syndrome or corresponding laboratory mutants have been cloned. One gene encodes a protein, RFX5, that is a member of the RFX family of DNA binding proteins. The other, CIITA, encodes a large protein with a defined acidic transcriptional activation domain; this protein does not interact with DNA. Expression plasmids encoding regions of RFX5 fused to the GAL4 DNA binding domain activated transcription from a reporter construct containing GAL4 sites in a cotransfection assay in the Raji human B cell line. However, these plasmids produced transcriptional activity in HeLa cells only in conjunction with interferon gamma stimulation, a condition in which expression of both CIITA and class II major histocompatibility complex surface proteins are induced. Furthermore, these plasmids were not active in RJ2.2.5, an in vitro mutagenized derivative of Raji in which both copies of CIITA are defective. Transcriptional activation by the RFX5 fusion protein could be restored in RJ2.2.5 by cotransfection with a CIITA expression plasmid. Finally, a direct interaction between RFX5 and CIITA was detected with the yeast two-hybrid and far-Western blot assays. Thus, RFX5 can activate transcription only in cooperation with CIITA. RFX5 and CIITA associate to form a complex capable of activating transcription from class II major histocompatibility complex promoters. In this complex, promoter specificity is determined by the DNA binding domain of RFX5 and the general transcription apparatus is recruited by the acidic activation domain of CIITA.

B-Lymphocytes↗

PubMed1992

Cloning of ndhK from soybean chloroplasts using antibodies raised to mitochondrial complex I.

A soybean shoot cDNA expression library was screened with polyclonal antibodies raised against red beet complex I and several clones were identified. One clone, consisting of a 1 kb insert, was fully sequenced. The sequence of 1025 bp was found to contain two extended open reading frames and the proteins encoded were identified as the ndhK and ndhJ products of the chloroplast genome. Nuclear, mitochondrial and chloroplast DNA was isolated and probed with a ndhK-specific probe. The chloroplast DNA contained a single copy of the cloned insert. With nuclear DNA, positively hybridising bands of 1.2, 2.7 and 3.2 kb were observed indicating that at least one gene homologous to ndhK of the chloroplast genome, is also present in the nucleus. The mitochondrial DNA did not hybridise with the ndhK probe. Western analysis of thylakoid proteins with the mitochondrial complex I antibodies revealed several bands. It is suggested that soybean contains two copies of the ndhK gene, one, on the plastid genome, coding for a subunit of a chloroplast NAD(P)H dehydrogenase, and the other, in the nucleus, coding for a subunit of mitochondrial complex I.

Amino Acid Sequence↗

PubMed1999

The cbb3 terminal oxidase of Rhodobacter sphaeroides 2.4.1: structural and functional implications for the regulation of spectral complex formation.

We have previously shown that the flow of reductant through the cbb3 terminal cytochrome c oxidase of Rhodobacter sphaeroides is essential to the repression of photosynthesis (PS) gene expression in the presence of oxygen by inhibiting the functional activity of the Prr two-component activation system. To gain further insight into the role of the cbb3 oxidase and the cognate ccoNOQP operon in the oxygen regulation of PS gene expression, we constructed nonpolar, in-frame deletions within the ccoN and ccoQ genes. Whereas mutations in ccoN, ccoQ, and ccoP resulted in PS gene expression in the presence of oxygen, only the ccoQ mutation showed both the normal flow of reductant through the cbb3 oxidase and the absence of any alteration in the relative levels of spheroidene and spheroidenone, as is observed for those mutations in the cco operon that result in the loss of terminal oxidase activity. Consistent with these findings is the observation that extra copies of the ccoNOQP operon in trans resulted in the decreased formation of both the B800-850 and B875 spectral complexes under anaerobic growth conditions. These results in conjunction with our earlier findings indicate that (1) the flow of reductant through the cbb3 terminal oxidase is a prerequisite to the regulation of PS gene expression by the Prr two-component regulatory system, (2) the CcoQ protein is involved in conveying the signal derived from reductant flow through the cbb3 terminal oxidase to the Prr regulatory pathway, (3) there is reductant flow through this terminal oxidase under anaerobic conditions, and as a result, the activity of the Prr system is still subject to cbb3 regulation, and (4) the acceptor for reductant flow through cbb3 under anaerobic conditions is in whole or in part involved in the conversion of spheroidene to spheroidenone.

Carotenoids↗