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PubMed2000

Simultaneous molecular karyotyping and mapping of viral DNA integration sites by 25-color COBRA-FISH.

Combined binary ratio labeling (COBRA) fluorescence in situ hybridization (FISH) allows 24-color FISH karyotyping of human metaphase chromosomes utilizing only four fluorochromes, instead of the five required for combinatorial labeling procedures. Here we show that by introduction of a fifth fluorochrome, COBRA-FISH permits molecular cytogenetic mapping of viral integration sites in complex karyotypes in the context of a 24-color hybridization. We were able to detect a single copy of the human papillomavirus 16 in the SiHa cell line and to confirm the site of integration at 13q21-31. We also demonstrate the gene mapping possibility of 25-color hybridization by detecting a MYC cosmid on normal metaphase chromosomes. The possibility of mapping single-copy probes in the background of 24-color hybridization expands the tools for cytogenetic mapping of DNA sequences and will contribute to the understanding of the role of viral integration and chromosome rearrangement in virus-mediated carcinogenesis.

Chromosomes, Human↗

PubMed2026

Tandem Duplication-Driven Neofunctionalization of UDP-Glycosyltransferases Shapes the Diversification of Triterpenoid Saponins in the Cucurbitaceae.

Tandem duplication of tailoring enzymes allows evolutionary innovation that diversifies plant specialized metabolism. Here, we present an interesting example of how tandem duplicated UDP-glycosyltransferases undergo neofunctionalization and shape the chemical diversity of triterpenoid saponins in the Cucurbitaceae family. A chromosome-level genome of Siraitia grosvenorii was assembled and aligned with multiple cucurbit genomes, revealing a specific UGT73AM tandem duplication responsible for regio-selective glycosylation (e.g. the rare 1,4-linked disaccharide) of diverse saponins such as mogrosides, ginsenosides, and momordicines. Comparative genomics depicted the evolutionary trajectory of a universal saponin-biosynthesizing UGT73 tandem arrays syntenously preserved across core eudicots, where lineage-specific UGT copies contribute to distinct metabolic phenotypes. A crystal structure of SgUGT73AM30 (mogrol 25-O-glycosyltransferase) in complex with UDP and mogrol was obtained to elucidate the molecular basis of the regio-specific decoration on vicinal diol of the substrates. Altogether, these findings provide insights into tandem duplication-driven diversification of glycosyltransferases and lay the foundation for engineered glycosylation of valuable triterpenoid saponins.

Saponins↗

PubMed2006

FISH and array-CGH analysis of a complex chromosome 3 aberration suggests that loss of CNTN4 and CRBN contributes to mental retardation in 3pter deletions.

Imbalances of 3p telomeric sequences cause 3p- and trisomy 3p syndrome, respectively, showing distinct, but also shared clinical features. No causative genes have been identified in trisomy 3p patients, but for the 3p- syndrome, there is growing evidence that monosomy for one or more of four genes at 3pter, CHL1, CNTN4, CRBN, and MEGAP/srGAP3, may play a causative role. We describe here an analysis of a complex chromosome 3p aberration in a severely mentally retarded patient that revealed two adjacent segments with different copy number gains and a distal deletion. The deletion in this patient included the loci for CHL1, CNTN4, and CRBN, and narrowed the critical segment associated with the 3p- syndrome to 1.5 Mb, including the loci for CNTN4 and CRBN. We speculate that the deletion contributes more to this patient's phenotype than the gains that were observed. We suggest that 3p- syndrome associated features are primarily caused by loss of CNTN4 and CRBN, with loss of CHL1 probably having an additional detrimental effect on the cognitive functioning of the present patient.

Adaptor Proteins, Signal Transducing↗

PubMed1995

Dissection of the core and auxiliary sequences in the vegetative replication origin of promiscuous plasmid RK2.

The vegetative replication origin (oriV) of promiscuous IncP plasmid RK2 can function in many Gram-negative bacterial species when supplied with the plasmid-encoded replication protein TrfA and host-encoded replication proteins including DnaA. Nine TrfA binding sites (iterons) are known, and also two DnaA binding sites, box 1, between TrfA iterons 4 and 5, and box 2, downstream of repeat 9. The deletion analysis presented here shows that the core oriV requires DnaA box 1 for function in Escherichia coli and Pseudomonas putida. This DnA box is not essential in Pseudomonas aeruginosa, although its deletion does reduce plasmid copy number in this species. A putative IHF binding site is located upstream of DnaA box 1, but IHF deficiency in E. coli seems not to alter replication efficiency or copy number control. Cloned oriV can interfere with maintenance of an independent RK2 replicon. Analysis of replication inhibition functions associated with oriV showed that a short putative orf between TrfA iterons 1 and 2 is not necessary for replication inhibition, the presence of repeats 5 to 9 in target and inhibitor plasmid are not sufficient for efficient inhibition and inhibition does not correlate directly with the number of direct repeats present. Rather, the results showed that the isolated repeats 1 and 2 to 4, potentiate replication inhibition disproportionately to their effect on the number of TrfA binding sites. The results are consistent with the idea that repeats 1 to 4, arranged as a single copy and as an irregular group of three, potentiate the ability of the oriV region to form complexes which inhibit replication. We suggest that TrfA bound at these iterons may be more susceptible to forming pairs between oriV sequences on different plasmids.

Bacterial Proteins↗

PubMed1996

Reexamination of the Sendai virus P protein domains required for RNA synthesis: a possible supplemental role for the P protein.

The Sendai virus P protein plays a central role in viral genome amplification and expression, forming complexes with the viral L protein to generate the polymerase (P-L) and unassembled N (P-N(o)). This latter complex prevents N from self-assembling illegitimately, i.e., independently of the concurrent assembly of a nascent viral genome, and is thought to represent the functional form of N in nucleocapsid assembly. Based upon earlier functional studies using an in vitro transcription/ replication system in which the P, L, and N proteins were coexpressed, we identified two regions of the P protein required for RNA synthesis, namely, the C-terminal 40% of the protein, and a second, apparently redundant domain near the N-terminus (either amino acids 1-77 or 78-145). The lack of sequence conservation in this second region, apart from overall negative charge, was reminiscent of the acidic activation domains of cellular transcription factors. However, we recently mapped a chaperone domain at the N-terminal of P (aa 33-41), which is required for stable complex formation with unassembled N(o) and, thus, for assembly and genome replication. In this present study we show that coexpression of N protein with P deletion mutants lacking this region (e.g., P delta 1-324) results in the sequestration of the mutant P by the illegitimately assembled form of N. As a consequence, P protein is unavailable for RNA synthesis from bona fide templates. We also find that in the absence of coexpressed N protein, the entire N-terminal 60% of the P protein is not required for mRNA synthesis. During these studies, a supplemental role for the P protein in viral RNA synthesis, independent of stable complex formation with L, was observed. This function involves, at least in part, the binding of additional copies of P to the N:RNA template.

Binding Sites↗

PubMed1995

Genetic evidence for the interaction of the yeast transcriptional co-activator proteins GCN5 and ADA2.

The GCN5 and ADA2 proteins are required for the activation function of a number of transcriptional activators in the yeast Saccharomyces cerevisiae. By using appropriate LexA fusion proteins we demonstrated that both proteins are required for part of the function of the GCN4, GAL4 and the VP16 transcriptional activation domains. Analysis of a gcn5 ada2 double disruption mutant did not reveal any additive effects, suggesting that the two proteins act in the same pathway. The GCN5 and ADA2 proteins can each activate transcription when directed to the promoter region of a reporter gene, but only in the presence of a wild-type ADA2 or GCN5 gene, respectively. The activation capacity is enhanced when the corresponding endogenous gene copy is disrupted. Taken together, these genetic data suggest that the two proteins interact and define one complex that mediates transcriptional activation. The function of this complex requires the bromodomain region of the GCN5 protein.

Cloning, Molecular↗

PubMed1996

DNA polymorphism among Fusarium oxysporum f.sp. elaeidis populations from oil palm, using a repeated and dispersed sequence "Palm".

A worldwide collection, of 76 F. oxysporum f.sp. elaeidis isolates (Foe), and of 21 F. oxysporum isolates from the soil of several palm grove was analysed by RFLP. As a probe, we used a random DNA fragment (probe 46) from a genomic library of a Foe isolate. This probe contains two different types of sequence, one being repeated and dispersed in the genome "Palm", the other being a single-copy sequence. All F. oxysporum isolates from the palm-grove soils were non-pathogenic to oil palm. They all had a simple restriction pattern with one band homologous to the single-copy sequence of probe 46. All Foe isolates were pathogenic to oil palm and they all had complex patterns due to hybridization with "Palm". This repetitive sequence reveals that Foe isolates are distinct from the other F. oxysporum palm-grove soils isolates. The sequence can reliably discriminate pathogenic from non-pathogenic oil palm isolates. Based on DNA fingerprint similarities, Foe populations were divided into ten groups consisting of isolates with the same geographic origin. Isolates from Brazil and Ecuador were an exception to that rule as they had the same restriction pattern as a few isolates from the Ivory Coast, suggesting they may originated from Africa.

Fusarium↗

PubMed1999

Nuclear gene defects in mitochondrial disorders.

An increasing number of nuclear genes have been associated with abnormalities of oxidative phosphorylation and mitochondrial disorders. The protein products of these genes can be grouped into three categories: structural components of the respiratory chain, factors influencing the structural integrity or the copy number of mitochondrial DNA, and proteins which control the formation, assembly and turnover of the respiratory complexes. Loss-of-function mutations in SURF-1, a gene belonging to the third category, have been associated with Leigh syndrome with cytochrome c oxidase deficiency. Mature Surf-1 protein (Surf-1p) is a 30 kDa hydrophobic polypeptide whose function is still unknown. Using antibodies against human Surf-1p, we demonstrated that this protein is imported into mitochondria as a larger precursor. The same analysis revealed that no protein is present in cell lines harboring loss-of-function mutations of SURF-1, regardless of their type and position. We also generated several constructs with truncated or partially deleted SURF-1 cDNAs. None of these constructs, expressed into SURF-1 null mutant cells, were able to rescue the COX phenotype, suggesting that different regions of the protein are all essential for function. Finally, experiments based on 2D gel electrophoresis indicated that assembly of COX in SURF-1 null mutants is blocked at an early step, most likely before the incorporation of subunit II in the nascent intermediates composed of subunit I alone or subunit I plus subunit IV.

Chromosomes, Human↗

PubMed1996

Biochemical analysis of the interaction of fibronectin with IgG and localization of the respective binding sites.

Fibronectin (Fn), a mosaic protein composed of multiple copies of three different module types (Fl, F2 and F3), has been found associated with circulating immune complexes (ICs) and immunoglobulin (Ig) aggregates in a variety of IC diseases and myeloproliferative disorders. We have previously shown that a proteolytic fragment of Mr = 25,900 Da, from the NH2-terminal domain of Fn, composed of five type 1 modules (1Fl -5Fl) binds to the major Ig classes under physiologic conditions, suggesting that the presence of Fn in ICs and cryoglobulins results from a physicochemical binding interaction between these two molecules. Using an ELISA, we now show that the interaction between Fn and IgG is: (1) not influenced by any other constituent of plasma; (2) unaffected by temperature; and (3) has an estimated Kd of 3.77 x 10(-9) M. In addition, we have further delineated the respective sites involved in the interaction between Fn and IgG. Recombinant type l module pairs (1Fl.2Fl and 4Fl.5Fl) from the NH2-terminus of Fn, expressed in yeast, were employed in an ELISA and affinity chromatography and compared with the 25.9 kDa (1Fl - 5Fl) fragment and intact Fn for binding to IgG. The 4Fl.5Fl and the 25.9 kDa fragment bound to immobilized IgG and inhibited Fn binding to IgG to nearly the same extent as the intact molecule (IC50: Fn = 6.77 x 1O(-9) M; 25.9 kDa fragment = 5 x 10(-9) M; 4Fl.5Fl = 7.6 x 10(-9) M). Thus, the binding site for IgG on the Fn molecule is localized to and completely conferred by the 4Fl.5Fl module pair (residues 151-244). Similar experiments using papain-generated Fab and Fc fragments of IgG localized the Fn binding site on IgG to the Fe region of the IgG molecule. Fn bound to the Fc fragment with a nearly identical Kd of 3.69 x 10(-9) M, as to intact IgG (3.77 x 10(-9) M). These studies support the hypothesis that the interaction between Fn and Ig may contribute to the pathophysiology of immune complex related disorders.

Binding Sites↗

PubMed1996

Open strands adjacent to iterons promote the binding of the replication initiator protein (Rep) of pSC101 to the unit sequence of the iterons in vitro.

The purified dimeric form of the Rep protein, a replication initiator protein of the plasmid pSC101, has a low affinity for repeated sequences, iterons, in the replication origin of the plasmid, and higher affinities for two inverted repeats in the operator region of the rep gene resulting in its functioning as an autorepressor. Studies of binding to various synthetic DNA have established that Rep can bind to duplex iteron-sequence carrying open (non-complementary) strands at one end proximal to the rep gene. Open strands at the opposite end of the iteron have no effect on Rep-binding. One open strand seems to be required in a sequence-specific fashion. A randomly sequenced duplex DNA with the open strands cannot bind to Rep but can function as a significant competitor. This suggests that Rep has some affinity for the open strands and forms a stable complex with the adjacent iteron. The mutated Rep protein, Rep1, which causes an increase in the plasmid copy number in vivo, has equally high affinity for the iteron with the open strands as wild type Rep, though it has a lower affinity for the inverted repeats than the wild type. The Rep dimer might bind to these DNA sequences with different modes.

Base Sequence↗

PubMed2005

Chromosome abnormalities in 10 lung cancer cell lines of the NCI-H series analyzed with spectral karyotyping.

The karyotypes of 10 lung cancer cell lines of the NCI-H series were analyzed with spectral karyotyping (SKY): 7 non-small lung cancer (NSCLC) lines and 3 small cell lung cancer (SCLC) lines. Modal chromosome number ranged from 42 (NCI-H2171) to 72 (NCI-H2126). All lines showed at least six structural abnormalities, and most had amplifications visible as double minutes or homogeneously staining regions (HSRs). Four reciprocal translocations were found: t(1;17)(p10;p10) in NCI-H82, t(3;6)(q24;q21) and t(12;17)(p10;p10) in NCI-H2009, and a complex t(2;6) in NCI-H1437. NCI-H1770 had a striking HSR containing many copies of the NMYC region. Karyotypes showed a wide range of relationship between numerical and structural change. Two of the lines showed little numerical change but many structural rearrangements (NCI-H209 with mode 46, but 12 rearrangements, and NCI-H2009 with mode 48 but 27 rearrangements). A second group had karyotypes that appeared to have evolved by unbalanced translocation leading to proportionate loss of chromosomes, with or without endoreduplication. In other lines, notably NCI-H2122, the structurally abnormal chromosomes appeared to have been added to a near-diploid karyotype. The karyotypes contribute to a full genomic characterization of these lines, almost all of which have matching normal lymphoblastoid cell lines.

Adenocarcinoma↗

PubMed2005

SCFGrr1-mediated ubiquitination of Gis4 modulates glucose response in yeast.

The F box protein Grr1 is the substrate specificity-determinant of the SCF(Grr1) E3 ubiquitin ligase complex. Genetic analyses of Grr1 mutants have implicated Grr1 in glucose repression, specifically with regard to expression of the SUC2 transcript. To better understand Grr1, we screened for substrates using a mutant version of Grr1 that should not associate with the SCF complex. We identified Gis4 as a novel Grr1 substrate. Gis4 was originally isolated as a multi-copy suppressor of a Gal--phenotype in the triple mutant snf1 mig1 srb8. Here, we show that Gis4 binds Grr1 in vivo and that Grr1 protein levels positively affect the protein levels of Gis4. The Gis4 protein is stable in wild-type cells and in grr1Delta cells; however, Gis4 is ubiquitinated in a Grr1-dependent manner. Furthermore, we show that Gis4 interacts with Snf1 in a Grr1-dependent fashion, and that Gis4 is involved in de-repression of SUC2 and in transcription of other Snf1-dependent transcripts. Gis4 appears to connect the glucose repression and de-repression pathways. We suggest that Gis4 may explain the glucose repression defects in carbon source metabolism for the grr1 mutants.

F-Box Proteins↗

PubMed2003

The new role of SAGE in gene discovery.

The sequencing of the human genome has led to in silico predictions of far fewer genes than anticipated. Recent studies using serial analysis of gene expression have cast doubt on this finding. One study predicts the presence of many unidentified low abundance transcripts, whereas two others have mapped unique tags to previously unpredicted exons. Genome and transcriptome complexity is thus greater than predicted and many of the missing genes are probably expressed in low copy numbers or only in early embryonic tissues.

Animals↗

PubMed2003

Close relationship between motor impairments and loss of functional motoneurons in a Charcot-Marie-Tooth type 1A model.

Charcot-Marie-Tooth disease type 1A is the most frequent hereditary neuropathy affecting the peripheral nervous system. A partial duplication of chromosome 17 (17p11.2) involving the PMP22 gene is responsible for dysmyelination-demyelination processes leading to motor and sensory impairments. Murine models of this disease are now widely used to investigate the mechanisms occurring at the behavioural and physiological levels. In this study, adult transgenic mice (6 months old) having integrated 7 copies of the human PMP22 gene were used to compare the motor performance, evaluated by using a complex locomotor test (the rotarod test), with both the number of functional motoneurons innervating the soleus muscle and the level of myelination in the sciatic nerve. Two levels of motor deficits were detected and led us to divide the population into two subgroups. In both impaired groups, the level of motor deficit was strongly correlated with the number of functional motoneurons evaluated by retrograde labeling from the muscle, but not with the number of myelinated fibers or the thickness of the myelin sheath (g-ratio). It therefore appears that the number of motor units may be a key element in motor impairments observed in Charcot-Marie-Tooth disease type 1A disease. These findings may have implications for therapeutic procedures, which should focus on the survival of the motoneuronal pool and/or the maintenance of functional neuro-muscular connexions to reduce motor impairments in humans.

Animals↗

PubMed1999

The RLF-B component of the replication licensing system is distinct from Cdc6 and functions after Cdc6 binds to chromatin.

Replication licensing factor (RLF) is an essential initiation factor that can prevent re-replication of DNA in a single cell cycle [1] [2]. It is required for the initiation of DNA replication, binds to chromatin early in the cell cycle, is removed from chromatin as DNA replicates and is unable to re-bind replicated chromatin until the following mitosis. Chromatography of RLF from Xenopus extracts has shown that it consists of two components termed RLF-B and RLF-M [3]. The RLF-M component consists of complexes of all six Xenopus minichromosome maintenance (MCM/P1) proteins (XMcm2-7), which bind to chromatin in late mitosis and are removed as replication occurs [3] [4] [5] [6] [7]. The identity of RLF-B is currently unknown. At least two factors must be present on chromatin before licensing can occur: the Xenopus origin recognition complex (XORC) [8] [9] and Xenopus Cdc6 (XCdc6) [10]. XORC saturates Xenopus sperm chromatin at approximately one copy per replication origin whereas XCdc6 binds to chromatin only if XORC is bound first [9] [10] [11]. Although XORC has been shown to be a distinct activity from RLF-B [9], the relationship between XCdc6 and RLF-B is currently unclear. Here, we show that active XCdc6 is loaded onto chromatin in extracts with defective RLF, and that both RLF-M and RLF-B are still required for the licensing of XCdc6-containing chromatin. Furthermore, RLF-B can be separated from XCdc6 by immunoprecipitation and standard chromatography. These experiments demonstrate that RLF-B is both functionally and physically distinct from XCdc6, and that XCdc6 is loaded onto chromatin before RLF-B function is executed.

Animals↗

PubMed1994

The testis-determining gene, SRY, exists in multiple copies in Old World rodents.

SRY is a unique gene on the Y chromosome in most mammalian species including the laboratory mouse, Mus musculus, and the closely related European wild mouse species M. spicilegus, M. macedonicus, and M. spretus. In contrast, SRY is present in 2-6 copies in the more distantly related Asian mouse species M. caroli, M. cervicolor, and M. cookii and in 2-13 copies in the related murid species Pyromys saxicola, Coelomys pahari, Nannomys minutoides, Mastomys natalensis, and Rattus norvegicus. Copy numbers do not correlate with known phylogenetic relationships suggesting that SRY has undergone a rapid and complex evolution in these species. SRY was recently proposed as a molecular probe for phylogenetic inferences. The presence of multiple SRY genes in a wide range of murid species and genera, and at least one cricetid species, necessitates caution in the use of SRY for phylogenetic studies in the Rodentia unless it is ascertained that multiple SRY genes do not exist.

Animals↗

PubMed2001

Molecular characterization of transgenic shallots (Allium cepa L.) by adaptor ligation PCR (AL-PCR) and sequencing of genomic DNA flanking T-DNA borders.

Genomic DNA blot hybridization is traditionally used to demonstrate that, via genetic transformation, foreign genes are integrated into host genomes. However, in large genome species, such as Allium cepa L., the use of genomic DNA blot hybridization is pushed towards its limits, because a considerable quantity of DNA is needed to obtain enough genome copies for a clear hybridization pattern. Furthermore, genomic DNA blot hybridization is a time-consuming method. Adaptor ligation PCR (AL-PCR) of genomic DNA flanking T-DNA borders does not have these drawbacks and seems to be an adequate alternative to genomic DNA blot hybridization. Using AL-PCR we proved that T-DNA was integrated into the A. cepa genome of three transgenic lines transformed with Agrobacterium tumefaciens EHA 105 (pCAMBIA 1301). The AL-PCR patterns obtained were specific and reproducible for a given transgenic line. The results showed that T-DNA integration took place and gave insight in the number of T-DNA copies present. Comparison of AL-PCR and previously obtained genomic DNA blot hybridization results pointed towards complex T-DNA integration patterns in some of the transgenic plants. After cloning and sequencing the AL-PCR products, the junctions between plant genomic DNA and the T-DNA insert could be analysed in great detail. For example it was shown that upon T-DNA integration a 66 bp genomic sequence was deleted, and no filler DNA was inserted. Primers located within the left and right flanking genomic DNA in transgenic shallot plants were used to recover the target site of T-DNA integration.

Base Sequence↗

PubMed1998

Regulation of expression of ribosomal protein L-21 genes of Entamoeba histolytica and E. dispar is at the post-transcriptional level.

Two genes, EhgLE3 and Ehg34, encoding the ribosomal protein L21 (rp-L21) were identified and characterized from Entamoeba histolytica. Their coding regions are highly conserved, but their flanking regions differ significantly. Analogous genes (EdgLE3 and Edg34) were characterized in E. dispar. The two rp-L21 copies are transcribed at similar levels in the two parasites. However, their relative binding to the polyribosomal complex during active translation is different. In E. histolytica, binding of EhgLE3 transcripts to the polyribosomes is significantly higher in comparison with that of Ehg34 transcripts, whereas in E. dispar the binding pattern is inverse. The importance of each of the rp-L21 flanking regions to gene translation was investigated by constructing hybrid plasmids containing the CAT reporter gene flanked by rp-L21 flanking regions. The plasmids were stably transfected into E. histolytica and E. dispar, and CAT mRNA and enzymatic activity levels were determined. All plasmids promoted transcription of CAT. Yet, in E. histolytica, high levels of CAT activity were observed only when gLE3 upstream regions flanked CAT. In contrast, in E. dispar, high levels of CAT activity were observed when g34 upstream regions flanked CAT. The downstream regions showed no significant effect on CAT translation.

Animals↗