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PubMed1991

IS801, an insertion sequence element isolated from Pseudomonas syringae pathovar phaseolicola.

A transposable element, designated IS801, was isolated from strain LR781 of Pseudomonas syringae pathovar phaseolicola in two independent events using the entrapment plasmid, pUCD800. IS801 is 1517 base pairs in length and contains open reading frames that potentially encode proteins of 311 and 172 amino acids, as well as smaller proteins. Unlike most other prokaryotic transposable elements, IS801 lacks terminal repeats. Sequence analysis revealed two target pentamers for IS801 insertion that differ by one base pair. One copy of IS801 generated a perfect duplication of its target, TGAAC. The second copy of IS801 was flanked by the target, TGGAC, at one end, and TGAAC at the other end. A third copy of IS801 was cloned from pMMC7105, an indigenous plasmid of strain LR781, and it was flanked by copies of the pentamer TGAAC.

Amino Acid Sequence↗

PubMed1997

Organization of the murine reduced folate carrier gene and identification of variant splice forms.

RT-PCR analysis of the reduced folate carrier (RFC) from L1210 and murine erythroleukemia cells led to the identification of three clones which appeared to result from the use of alternative splice sites. The nucleotide sequence of each splice form predicts a protein that contains at least the first 7 transmembrane domains of the parental RFC protein followed by a novel hydrophilic carboxyl terminus of 33, 72, or 105 amino acid residues. Sequence analysis of cDNA clones isolated from murine liver and the results of 5'-RACE from L1210 cells indicated that RFC also utilizes alternate 5'-terminal exons. To understand how the alternatively spliced RFC transcripts and multiple 5'-termini were generated, the genomic organization of RFC was determined. The gene is comprised of at least 8 exons, the first two of which encode the alternative 5' termini. Based on sequence identity with cDNAs encoding RFC from hamster and rat, however, it appears that additional 5' exons may be present. Two of the RFC splice variants result from the use of a cryptic splice donor site within exon 4 and the third results from the use of a cryptic splice acceptor site within exon 5. In addition, the splice variant form that encodes the largest protein also utilizes an alternative exon located between exons 5 and 6. The apparent use of alternative transcriptional start sites and the identification of several RFC splice forms raises the possibility that unique RFC molecules may be generated that exhibit tissue- or cell line-specific distribution.

Alternative Splicing↗

PubMed1980

The white pock (mu) mutants of rabbit poxvirus. III. Terminal DNA sequence duplication and transposition in rabbit poxvirus.

The restriction fragment patterns of the DNA of three white pock (mu) nonhost range mutants RPmu mutants) of rabbit poxvirus (RPV) show the presence of net insertions of DNA. Two of the mutants (RPmu21 and RPmu7) contain two molar quantities of 13 X 10(6) and 15 X 10(6) daltons, respectively, of the left-most viral DNA sequences. The extra copy of these sequences was inserted into the right-most region of the viral genome which in both cases had been modified by deletion of 10 X 10(6) daltons of the original extreme right-most DNA sequences. Hence two mutants with "left-hand" mirror image termini of 13 X 10(6) and 15 X 10(6) daltons of DNA were generated with an overall net increase in mass of 3 X 10(6) and 5 X 10(6) daltons of DNA to yield genome molecular weights of 121 X 10(6) and 123 X 10(6) for RPmu21 and 7, respectively. A third mutant (RPmu81g) contained 28 X 10(6) daltons of the right-most parental DNA sequences inserted into the left end of the genome, which had deleted 6 X 10(6) daltons of the extreme left-hand sequences. This variant contains "right-hand" mirror image termini of 28 X 10(6) daltons of DNA and a net increase in molecular weight of 22 X 10(6) daltons of DNA to yield a genome molecular weight of 140 X 10(6). The cross-linked end of the transposed sequences is retained in all cases. Our data suggest that the terminal DNA sequences at either end of the virus are not essential for a productive infection in certain host cells and that the pathogenicity of orthopoxviruses may be related in part to a series of varied and interchangeable DNA sequences located at both extremes of a high conserved genome core.

Base Sequence↗

PubMed1996

Steroid sulfotransferases.

Human dehydroepiandrosterone sulfotransferase (DHEA-ST) catalyzes the sulfonation of DHEA, cholesterol, pregnenolone as well as androsterone. RNA blot analysis shows two DHEA-ST mRNA species of 1.3 and 1.8 kb that are expressed similarly in liver and adrenals. To determine whether the form expressed in adrenals is distinct or identical with the one expressed in liver, we have cloned and sequenced the 1.8 kb DHEA-ST cDNA from human adrenal cDNA library. Except for one nucleotide difference, the human adrenal and liver DHEA-ST cDNAs are identical. Using expression vectors containing the chloramphenicol acetyltransferase (CAT) reporter gene ligated to various fragments of the DHEA-ST gene promoter, we have shown that DHEA-ST gene promoter activity is stimulated by estradiol (E2). The E2 stimulation is inhibited by the anti-estrogen EM-139. In contrast to human DHEA-ST, guinea pig hydroxysteroid sulfotransferases show high substrate- and stereo-selectivity. We have cloned a chiral-specific pregnenolone sulfotransferase (PREG-ST) which catalyzes mainly the transformation of pregnenolone to pregnenolone sulfate. Estrogen sulfotransferase catalyzes the conversion of estrone and estradiol to their inactive sulfated forms and could thus play a major role in the control of estrogen levels in target tissues. Recently, using a probe derived from bovine estrogen sulfotransferase, we have cloned a cDNA and gene that we first named human estrogen sulfotransferase (hEST) since the expressed enzyme is able to transform estrone to estrone sulfate. Actually, the Hugo nomenclature committee named this gene STM gene because it also codes for monoamine-sulfating phenol-sulfotransferase (M-PST). hEST1 possesses the same coding and 3'-untranslated region as human brain aryl sulfotransferase (HAST) and M-PST, but different 5'-noncoding region. Analysis of hEST1 gene sequence indicates that hEST1 and HAST3 or M-PST mRNA species are transcribed from a single hEST1 gene by alternative promoters using two separate exon 1, named exon Ia and exon Ib. We also described the identification of a third mRNA species (M-PST gamma) issued from the STM gene and the characterization of the structure of the phenol-sulfating phenolsulfotransferase (STP) gene that is highly homologous to the STM gene. Similar to STM, the STP gene generates multiple mRNA species that differ only in the 5'-untranslated sequence.

Adrenal Glands↗

PubMed1999

Taking MAD to the extreme: ultrafast protein structure determination.

Multiwavelength anomalous diffraction data were measured in 23 min from a 16 kDa selenomethionyl substituted protein, producing experimental phases to 2.25 A resolution. The data were collected on a mosaic 3 x 3 charge-coupled device using undulator radiation from the Structural Biology Center 19ID beamline at the Argonne National Laboratory's Advanced Photon Source. The phases were independently obtained semiautomatically by two crystallographic program suites, CCP4 and CNS. The quality and speed of this data acquisition exemplify the opportunities at third-generation synchrotron sources for high-throughput protein crystal structure determination.

Base Sequence↗

PubMed1999

Role of multiple gene copies in particulate methane monooxygenase activity in the methane-oxidizing bacterium Methylococcus capsulatus Bath.

Genes for the subunits of particulate methane monooxygenase, PmoABC, have been sequenced from the gamma-proteobacterial methanotroph Methylococcus capsulatus Bath. M. capsulatus Bath contains two complete copies of pmoCAB, as well as a third copy of pmoC. The two pmoCAB regions were almost identical at the nucleotide sequence level, differing in only 13 positions in 3183 bp. At the amino acid level, each translated gene product contained only one differing residue in each copy. However, the pmoC3 sequence was more divergent from the two other pmoC copies at both the far N-terminus and far C-terminus. Chromosomal insertion mutations were generated in all seven genes. Null mutants could not be obtained for pmoC3, suggesting that it may play an essential role in growth on methane. Null mutants were obtained for pmoC1, pmoC2, pmoA1, pmoA2, pmoB1 and pmoB2. All of these mutants grew on methane, demonstrating that both gene copies were functional. Copy 1 mutants showed about two-thirds of the wild-type whole-cell methane oxidation rate, while copy 2 mutants showed only about one-third of the wild-type rate, indicating that both gene copies were necessary for wild-type particulate methane monooxygenase activity. It was not possible to obtain double null mutants that were defective in both pmo copies, which may indicate that some expression of pMMO is important for growth.

Amino Acid Sequence↗

PubMed1992

Sequence evolution in mitochondrial ribosomal and ND-1 genes in lepidoptera: implications for phylogenetic analyses.

A 2,256-bp sequence of the mitochondrial genome of a lepidopteran (Spodoptera frugiperda) contains tRNAs for valine and leucine, the 16S rRNA, and three-quarters of the ND-1 presumptive protein-coding gene. A 64-bp stretch of unknown function was located between the rRNA and leucine tRNA. Sequence divergence in the 16S rRNA obtained from alignment with published insect sequences is consistent with phylogenetic hypotheses, in that Diptera and Lepidoptera are more closely related to each other (24% sequence divergence) than either is to Hymenoptera (31%). Within the ND-1 gene, sequences for four additional Lepidoptera were generated for a 314-bp region and contrasted with published sequences for the locust and Drosophila. Sequence divergence in this region was consistent with accepted phylogenetic relationships, but results of parsimony analyses were not. Cladograms consistently recovered accepted higher level relationships (monophyly of Lepidoptera), despite high homoplasy, but were unable to resolve superfamily and family relationships within Lepidoptera, regardless of the outgroup or character subset analyzed. Character analysis indicated that homoplasy was decreased at higher levels when first- and second-codon sites were used exclusively. At the lowest level (families), resolution was enhanced by inclusion of third-codon sites. Inability of molecular data to recover a well-established phylogeny may be rectified by additional characters or taxa, but it is clear that homoplasy is sufficiently high to caution against the acceptance of relationships generated with this molecular region that are not extremely robust.

Amino Acid Sequence↗

PubMed1998

Evidence for a new transcript of the Epstein-Barr virus/C3d receptor (CR2, CD21) which is due to alternative exon usage.

CR2 extracellular domain is constituted of 15 or 16 Short Consensus Repeats (SCR), with additional SCR 11 localized between SCRs 10 and 12. We amplified Raji cDNA library, with specific primers where SCR 11 is localized. This generated a new fragment of 643 bp (16b SCR), in addition to the two expected transcripts of 489 (15 SCR) and 667 (16a SCR) bp. Sequencing these three fragments and the corresponding genomic DNA, demonstrated the presence of a 24 bp deletion in 16b SCR, without change of open reading frame and that this 24 bp region was flanked by two splicing acceptor sites. This supported a new alternative splicing of CR2, with generation of a third distinct mRNA. This third transcript was expressed in human CR2 positive T cells, normal or transformed B cells and EBV negative B cell lines. The 24 bp deletion corresponds to a proline-rich region, which may influence CR2 conformation and more likely have consequences on CR2 extra and intracellular interactions.

Alternative Splicing↗

PubMed2002

Identification of resistance gene analogs linked to a powdery mildew resistance locus in grapevine.

Oligonucleotide primers, designed to conserved regions of nucleotide binding site (NBS) motifs within previously cloned pathogen resistance genes, were used to amplify resistance gene analogs (RGAs) from grapevine. Twenty eight unique grapevine RGA sequences were identified and subdivided into 22 groups on the basis of nucleic acid sequence-identity of approximately 70% or greater. Representatives from each group were used in a bulked segregant analysis strategy to screen for restriction fragment length polymorphisms linked to the powdery mildew resistance locus, Run1, introgressed into Vitis vinifera L. from the wild grape species Muscadinia rotundifolia. Three RGA markers were found to be tightly linked to the Run1 locus. Of these markers, two (GLP1-12 and MHD145) cosegregated with the resistance phenotype in 167 progeny tested, whereas the third marker (MHD98) was mapped to a position 2.4 cM from the Run1 locus. The results demonstrate the usefulness of RGA sequences, when used in combination with bulked segregant analysis, to rapidly generate markers tightly linked to resistance loci in crop species.

Journal Article↗

PubMed1997

Determination of hepatitis C virus genotypes in the United States by cleavase fragment length polymorphism analysis.

We describe the application of a new DNA-scanning method, which has been termed Cleavase Fragment Length Polymorphism (CFLP; Third Wave Technologies, Inc., Madison, Wis.), for the determination of the genotype of hepatitis C virus (HCV). CFLP analysis results in the generation of structural fingerprints that allow discrimination of different DNA sequences. We analyzed 251-bp cDNA products generated by reverse transcription-PCR of the well-conserved 5'-noncoding region of HCV. We determined the genotypes of 87 samples by DNA sequencing and found isolates representing 98% of the types typically encountered in the United States, i.e., types 1a, 1b, 2a/c, 2b, 3a, and 4. Blinded CFLP analysis of these samples was 100% concordant with DNA sequencing results, such that closely related genotypes yielded patterns with strong familial resemblance whereas more divergent sequences yielded patterns with pronounced dissimilarities. In each case, the aggregate pattern was indicative of genotypic grouping, while finer changes suggested subgenotypic differences. We also assessed the reproducibility of CFLP analysis in HCV genotyping by analyzing three distinct isolates belonging to a single subtype. These three isolates yielded indistinguishable CFLP patterns, as did replicate analysis of a single isolate. This study demonstrates the suitability of this technology for HCV genotyping and suggests that it may provide a low-cost, high-throughput alternative to DNA sequencing or other, more costly or cumbersome genotyping approaches.

Base Sequence↗

PubMed1997

Clinical, biochemical, and molecular investigations of a genetic isolate of growth hormone insensitivity (Laron's syndrome).

We have characterized the GH receptor mutation that is responsible for extreme short stature and GH insensitivity in a Bahamian genetic isolate. Heights of affected individuals ranged from -4.0 to -6.3 SD. Like others with Laron's syndrome, they had normal to high serum GH concentrations and low serum insulin-like growth factor I concentrations. Circulating levels of GH-binding protein activity were below limits of detection. Amplification of exons 2-7 and screening with single strand conformational polymorphism analysis located an abnormality in exon 7. Sequencing identified homozygosity for a C to T transition in the third position of codon 236. Reverse transcription and PCR amplification of complementary DNA from lymphocytes showed that this same sense mutation generated a new splice donor site 63 bp 5' to the normal exon 7 splice site. This novel site was used to the exclusion of the normal site in homozygotes. Both normal and variant messenger ribonucleic acid species were detected in heterozygotes. The predicted protein lacks 21 amino acids, including those defining the WS-like motif of the GH receptor extracellular domain. The high frequency of Laron's syndrome in this isolated island population probably reflects the introduction of the G236 splice mutation by a settler early in the 300-yr history of English settlement.

Adolescent↗

PubMed1992

VH gene rearrangement events can modify the immunoglobulin heavy chain during progression of B-lineage acute lymphoblastic leukemia.

The presence of multiple VHDJH joinings in upwards of 30% of acute lymphoblastic leukemias (ALL) suggests a relative instability of the rearranged immunoglobulin heavy chain (IgH) gene, but the mechanisms involved are not completely understood. An investigation of the structure of the VHDJH joinings using complementarity determining region (CDR)3 polymerase chain reaction (PCR) in 12 leukemias at both diagnosis and relapse indicates that this instability may increase as a function of time. In only one of seven cases in which relapse occurred within 3 years from diagnosis was a new VHDJH joining identified and this coexisted with the original diagnostic joining. Most strikingly, new VHDJH joinings were identified in four of five cases in which relapse occurred more than 5 years from diagnosis. In this latter population, the instability of the joinings was generated from VH----VH gene replacement events in two cases, since the new joinings retained the original DJH sequences and partial N region homology at the VHD junction, and probably in a third case from a VH gene rearrangement to a common DJH precursor. Furthermore, in five of 23 (21.7%) additional cases studied at diagnosis, subclones were identified that had similar modifications of the VH-N region. These data indicate that VH gene replacement events and VH gene rearrangements to a common DJH joining contribute to the instability of the VHDJH joining in ALL. This phenomenon should be taken into consideration in those methodologies that exploit IgH rearrangements for detection of minimal residual disease.

Adolescent↗

PubMed1991

Characterization of immunoglobulin heavy chain genes from an acute lymphocytic leukemia with four rearrangements.

Approximately 25% of acute leukemias of the B-cell lineage demonstrate more than two rearranged immunoglobulin heavy chain genes when examined by Southern blot analysis. The origin of the extra bands was investigated by molecular cloning and sequencing of four rearranged genes from one patient's leukemic cells. All four rearrangements were apparently derived independently. Two of the rearrangements used the VH6 variable region, attached to different diversity and joining regions. One of the two rearrangements contained a mutation in the coding sequence leading to the generation of a nonsense codon. This rearranged gene also differed from the other VH6 containing gene starting at about 330 bp upstream of the ATG initiation codon. The third rearranged gene used a member of the VH2 variable gene family. A DH-JH rearrangement was found in the fourth rearranged gene. The data indicate that the leukemia probably arose as a result of the transformation of an early B-cell progenitor that lacked rearranged immunoglobulin genes but retained some differentiation potential.

Blotting, Southern↗

PubMed1985

Developmental changes in the understanding of temporal sequence.

In 3 experiments, 4-, 5-, and 6-year-olds' ability to sequence events was examined. We hypothesized that children initially construct temporal sequences by relying on the organization of their world knowledge instead of inferring logical relations among actions. In the first experiment, children generated picture sequences of familiar and unfamiliar events in forward and backward order without having seen the pictures in their correct sequence. In the second experiment, children reconstructed previously seen sequences, and in the third experiment, children were shown forward and backward sequences and reconstructed them in the opposite direction. Across experiments, the same pattern of performance was found; familiar events in forward order were the easiest to sequence, then unfamiliar events in forward order, familiar events in backward order, and finally unfamiliar events in backward order. These results are discussed along with other findings suggesting a similar pattern of performance across a wide developmental age span.

Child↗

PubMed1995

The structure of the bovine cathepsin B gene. Genetic variability in the 3' untranslated region.

Cathepsin B is a cysteine proteinase which plays an important role in lysosomal proteolysis. We report here the characterization of a 15-kbp genomic clone of the bovine cathepsin B gene. Bovine preprocathepsin B is encoded by nine exons from translational initiation to stop codon. The last exon is sandwiched between Alu-like short interspersed nuclear elements. Alternate use of polyadenylation sites generates three transcripts encoding bovine cathepsin B. In all tissues tested, 3' end cleavage was found to occur in equal proportion at the first and second polyadenylation site, producing transcripts of 2.6-kb. Polyadenylation at the third polyadenylation site generates a 3.2-kb mRNA, only expressed at low levels and in a developmental and tissue-specific manner. Due to micro-heterogeneities between genomic and cDNA clones, sequence polymorphism was investigated in the trailer region. DNA sequencing of PCR-amplified genomic fragments revealed that, in contrast to the protein-encoding region, genetic variability exists in the 3' untranslated region. Polymorphism in the trailer was confirmed in cathepsin B mRNA by ribonuclease-protection assays. We finally emphasize that while exon-exon boundaries in mature cathepsin B are well conserved from nematodes to mammals, exons also tend to correspond to discrete units of cathepsin B structure.

Amino Acid Sequence↗

PubMed2005

An outbreak of SHV-5 producing Klebsiella pneumoniae in a neonatal intensive care unit; meropenem failed to avoid fecal colonization.

An outbreak of extended-spectrum beta-lactamase (ESBL) producing Klebsiella pneumoniae (ESBL-Kp) in a neonatal intensive care unit prompted a prospective surveillance study between 12th September and 6th October 2003. Surveillance was carried out by obtaining stool samples twice a week. The DNA relatedness of the isolates was shown by random amplified polymorphic DNA comparison (ERIC-PCR). ESBL production was identified by clavulanate synergy, isoelectric focusing, PCR and sequence analysis. During the study period, 49 neonates were hospitalized in the neonatal intensive care unit (NICU). In the first 20-day period, five neonates were infected with ESBL-Kp. The first patient treated with third generation cephalosporin and the second patient treated with meropenem died. While all three infected survivors were clinically improving, the digestive tracts were being colonized by SHV-5 producing Klebsiella. In the next period of the study, five neonates were colonized by ESBL-Kp as well. Univariate comparison of risk factors between colonized and non-colonized neonates was not significant. A total of 24 colonally related ESBL-Kp have been recovered from clinical materials and stool samples. This study demonstrated that parenterally applied meropenem, though successful in treating the systemic illness, might fail to protect the digestive tract from colonization of ESBL-Kp.

Anti-Bacterial Agents↗

PubMed2000

Haplotype dimorphism in a SNP collection from Drosophila melanogaster.

A moderate resolution single nucleotide polymorphism (SNP) map of the genome of Drosophila melanogaster that is designed for use in quantitative genetic mapping is described. Seventeen approximately 500 nucleotide gene sequences spaced at 10 to 20 centimorgan intervals were combined with 49 shorter sequence tag sites (STSs) at 5 to 10 centimorgan intervals to generate a map that should not leave any gaps greater than one half of a chromosome arm when any two wild type lines are compared. Of 20 markers with sufficient polymorphism to construct haplotype cladograms, 13 showed evidence for two divergent classes of haplotype. The possible mechanisms for and implications of the unexpected finding that two thirds of all short gene sequences in D. melanogaster may be dimorphic are discussed, including the suggestion that admixture between two separate lineages may have been a major event in the history of the species.

Animals↗

PubMed1985

The FLP recombinase of the 2 micron circle DNA of yeast: interaction with its target sequences.

We have studied the interaction of purified FLP protein with restriction fragments from the substrate 2mu circle DNA of yeast. We find that FLP protects about 50 bp of DNA from nonspecific nuclease digestion. The protected site consists of two 13 bp inverted repeat sequences separated by an 8 bp spacer region. A third 13 bp element is also protected by binding of the FLP protein. We demonstrate that FLP introduces single- and double-strand breaks into the substrate DNA. This site-specific cleavage occurs at the margins of the spacer region, generating 8 bp 5' protruding ends with 5'-OH and 3'-protein-bound termini. Binding to mutant sites and half-sites demonstrates that the third symmetry element is not important for binding and cleavage by the FLP protein. The integrity of the core region is important for the cleavage activity of FLP.

Base Composition↗