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PubMed1991

A superfamily of Arabidopsis thaliana retrotransposons.

We describe a superfamily of Arabidopsis thaliana retrotransposable elements that consists of at least ten related families designated Ta1-Ta10. The Ta1 family has been described previously. Two genomic clones representing the Ta2 and Ta3 elements were isolated from an A. thaliana (race Landsberg erecta) lambda library using sequences derived from the reverse transcriptase region of Ta1 as hybridization probes. Nucleotide sequence analysis showed that the Ta1, Ta2 and Ta3 families share greater than 75% amino acid identity in pairwise comparisons of their reverse transcriptase and RNase H genes. In addition to Ta1, Ta2 and Ta3, we identified seven other related retrotransposon families in Landsberg erecta, Ta4-Ta10, using degenerate primers and the polymerase chain reaction to amplify a highly conserved region of retrotransposon-encoded reverse transcriptase. One to two copies of elements Ta2-Ta10 are present in the genomes of the A. thaliana races Landsberg erecta and Columbia indicating that the superfamily comprises at least 0.1% of the A. thaliana genome. The nucleotide sequences of the reverse transcriptase regions of the ten element families place them in the category of copia-like retrotransposons and phylogenetic analysis of the amino acid sequences suggests that horizontal transfer may have played a role in their evolution.

Amino Acid Sequence↗
PubMed1992

Global population genetic structure and male-mediated gene flow in the green turtle (Chelonia mydas): RFLP analyses of anonymous nuclear loci.

We introduce an approach for the analysis of Mendelian polymorphisms in nuclear DNA (nDNA), using restriction fragment patterns from anonymous single-copy regions amplified by the polymerase chain reaction, and apply this method to the elucidation of population structure and gene flow in the endangered green turtle, Chelonia mydas. Seven anonymous clones isolated from a total cell DNA library were sequenced to generate primers for the amplification of nDNA fragments. Nine individuals were screened for restriction site polymorphisms at these seven loci, using 40 endonucleases. Two loci were monomorphic, while the remainder exhibited a total of nine polymorphic restriction sites and three size variants (reflecting 600-base pair (bp) and 20-bp deletions and a 20-bp insertion). A total of 256 turtle specimens from 15 nesting populations worldwide were then scored for these polymorphisms. Genotypic proportions within populations were in accord with Hardy-Weinberg expectations. Strong linkage disequilibrium observed among polymorphic sites within loci enabled multisite haplotype assignments. Estimates of the standardized variance in haplotype frequency among global collections (FST = 0.17), within the Atlantic-Mediterranean (FST = 0.13), and within the Indian-Pacific (FST = 0.13), revealed a moderate degree of population substructure. Although a previous study concluded that nesting populations appear to be highly structured with respect to female (mitochondrial DNA) lineages, estimates of Nm based on nDNA data from this study indicate moderate rates of male-mediated gene flow. A positive relationship between genetic similarity and geographic proximity suggests historical connections and/or contemporary gene flow between particular rookery populations, likely via matings on overlapping feeding grounds, migration corridors or nonnatal rookeries.

Animals↗
PubMed1989

Evolutionary comparison of the avian IgL locus: combinatorial diversity plays a role in the generation of the antibody repertoire in some avian species.

Immunoglobulin light chain (IgL) diversity is generated in the chicken by recombination between the single functional variable (VL) and joining (JL) gene segments and subsequent somatic diversification of the rearranged VL region. In order to determine whether these events are a general feature of avian IgL genes, we analyzed the organization and recombinatorial characteristics of the IgL loci of several other avian species. Southern blot analysis of bursal and germline DNA using chicken VL and constant (CL) probes revealed that the IgL loci of quail, mallard duck, pigeon, turkey, cormorant, and hawk consist of a family of VL elements, but undergo a single major rearrangement event similar to that observed in chickens. In contrast, several rearrangements were observed in the Muscovy duck locus. A phage clone containing a 26 kb insert that hybridized to VL and CL probes was isolated from a Muscovy duck erythrocyte DNA genomic library. Nucleotide sequencing revealed that the clone contained a single JL-CL region flanked on the 5' side by five VL segments. Unlike the chicken, two of the VL segments (VL1, VL5) appear to be functional. The remaining three VL segments are pseudogenes that lack promoter and leader sequences, but one of these (psi VL3) has recombination signal sequences. Overall, these data indicate that rearrangement of one VL gene segment is a general feature of the IgL locus in many avian species. In these species, the presence of a family of VL elements that do not rearrange suggests that a pseudogene pool may be available for somatic diversification by gene conversion. The organization of the Muscovy duck IgL locus suggests that additional combinatiorial diversity has evolved independently in some avian species.

Amino Acid Sequence↗
PubMed2005

Isolation of a Drosophila gene coding for a protein containing a novel phosphatidylserine-binding motif.

To elucidate the molecular basis of the binding of proteins to the membrane phospholipid phosphatidylserine (PS), we characterized PS-binding peptides isolated from a phage display library. Amino acid sequences deduced from the nucleotide sequences of over 60 phage clones isolated revealed that there was no common primary structure among these peptides, but all peptides were rich in basic amino acid residues. In particular, 15 clones encoded peptides that contained contiguous arginine residues. Characterization of two such peptides in more detail showed that they bound to PS, and to a much lower extent to other phospholipids, including phosphatidylinositol, phosphatidylethanolamine, and phosphatidylcholine. Unlike other Ca2+-dependent PS-binding proteins, these peptides did not require Ca2+ for binding to PS, and the addition of Ca2+ did not alter the phospholipid specificity. Substitution of one of the two RR sequences in one peptide by alanine had no effect, but that of both sequences completely abolished the activity. Furthermore, we identified a Drosophila gene coding for a presumed nuclear protein that shares an amino acid sequence, including a RR residue, with one of the two PS-binding peptides. This protein bound to PS partly depending on the presence of the RR residue. These results allowed us to conclude that an amino acid sequence including contiguous arginine residues is a novel motif that defines Ca2+-independent PS-binding activity.

Amino Acid Motifs↗
PubMed1983

The chicken H5 gene is unlinked to core and H1 histone genes.

An H5 cDNA clone was used to select H5 genomal recombinants from a chicken Charon 4A library. DNA sequence analysis shows that the H5 gene contains no introns. Putative 5' promoter elements and a 3' polyadenylation site are present within the 1.8 kb of DNA examined. Analysis of 41 kb of DNA surrounding the H5 gene shows that it is not closely linked to either H1 or core histone genes.Images

Amino Acid Sequence↗
PubMed1985

Primary structure of the soybean nodulin-23 gene and potential regulatory elements in the 5'-flanking regions of nodulin and leghemoglobin genes.

The nodulin-23 gene of soybean is one of the most abundantly transcribed genes induced during symbiosis with Rhizobium. Using a plasmid (pNod25) from a nodule cDNA library, we have isolated the nodulin-23 gene from a soybean genomic library. Nucleotide sequence analysis of the cDNA and of the genomic clone indicated that the coding region of this gene is 669 bp long and is interrupted by a single intron of about 530 bp. The deduced protein sequence suggests that nodulin-23 may have a signal sequence. The 5'-flanking sequence of two other nodulin genes, nodulin-24 encoding for a membrane polypeptide and one of the leghemoglobin genes (LbC3), were obtained. Comparison of these sequences revealed three conserved regions, one of which, an octanucleotide (GTTTCCCT), has 100% homology. The conserved sequences are arranged in a unique fashion and have a spatial organization with respect to order and position, which may suggest a potential regulatory role in controlling the expression of nodulin and leghemoglobin genes during symbiosis.

Amino Acid Sequence↗
PubMed1986

Functional, developmentally expressed genes for mouse U1a and U1b snRNAs contain both conserved and non-conserved transcription signals.

Four genes that encode mouse U1a1, U1b2 and U1b6 snRNAs have been isolated from a mouse genomic DNA library. They all appear to be functional U1 genes since they are accurately transcribed into full length, capped snRNAs upon injection into Xenopus oocytes. A mouse pseudogene that is not transcribed in Xenopus oocytes was also isolated from the mouse genomic library. DNA sequence analysis of the 5' and 3' flanking regions of the functional genes revealed the presence of three highly conserved sequence elements that have been shown to be required for transcription initiation or 3' end formation in other U1 genes. Each of these U1 RNA genes also contains non-conserved sequences in the 5' flanking region that could function in their controlled expression during development.

Animals↗
PubMed1990

Structure and transcription of a human gene for H1 RNA, the RNA component of human RNase P.

The gene coding for H1 RNA, the RNA component of human RNase P, has been isolated and characterized from a human genomic DNA library. The sequence corresponding to the mature H1 RNA is almost identical to that previously identified using H1 RNA and a cDNA clone corresponding to it. The nucleotide sequence of the genomic clone contains an array of potential transcriptional control elements, some characteristic of transcription by RNA polymerase III and some characteristic of RNA polymerase II, as is also the case for U6 and certain other small stable RNAs. The transcription in vitro of the genomic clone shows that the gene is functional and is transcribed by RNA polymerase III. Southern hybridization analysis indicates that there is very likely only one copy of the gene for H1 RNA in the human genome.

Base Sequence↗
PubMed1990

Mouse U14 snRNA is encoded in an intron of the mouse cognate hsc70 heat shock gene.

Mouse U14 snRNA (previously designated mouse 4.5S hybRNA) is an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA (1). A single genomic fragment of mouse DNA containing the U14 snRNA gene(s) has been isolated from a Charon 4A lambda phage mouse genomic library and sequenced. Results have surprisingly revealed the presence of three U14 snRNA-homologous regions positioned within introns 5, 6, and 8 of the mouse cognate hsc70 heat shock gene. Comparative analysis with the previously reported rat and human cognate hsc70 genes revealed a similar positioning of U14 snRNA-homologous sequences within introns 5, 6 and 8 of the respective rat and human genes. The U14 sequences contained in all three introns of all three organisms are highly homologous to each other and well conserved with respect to the diverging intron sequences flanking each U14-homologous sequence. Comparison of the mouse U14 snRNA sequence with the U14 DNA sequences contained in the three mouse hsc70 introns indicates that intron 5 is utilized for U14 snRNA synthesis in normally growing mouse ascites cells. Analysis of the determined mouse, rat, and human U14-homologous sequences and the upstream and downstream flanking regions did not reveal the presence of any previously defined RNA polymerase I, II, or III binding sites. This suggests that either higher eukaryotic U14 snRNA is transcribed from a unique transcriptional promoter sequence, or alternatively, is generated by intron processing of the hsc70 pre-mRNA transcript.

Amino Acid Sequence↗
PubMed1995

Mouse silver mutation is caused by a single base insertion in the putative cytoplasmic domain of Pmel 17.

This laboratory has established in previous studies that Pmel 17, a gene expressed specifically in melanocytes, maps near the silver coat color locus (si/si) on mouse chromosome 10. In the current study, we have focused on determining whether or not the si allele carries a mutation in Pmel 17. Pmel 17 cDNA clones, isolated from wild-type and si/si murine melanocyte cDNA libraries, were sequenced and compared. A single nucleotide (A) insertion was found in the putative cytoplasmic tail of the si/si Pmel 17 cDNA clone. This insertion is predicted to alter the last 24 amino acids at the C-terminus. Also predicted is the extension of the Pmel 17 protein by 12 residues because a new termination signal created downstream from the wild-type reading frame. The mutation was confirmed by the sequence of the PCR-amplified genomic region flanking and including the mutation site. The fact that si/si Pmel 17 was not recognized by antibodies directed toward the C-terminal 15 amino acids of wild-type Pmel 17, indicated a defect in this region. We conclude from these results that silver pmel 17 protein has a major defect at the carboxyl terminus. The chromosomal location and the identification of a potentially pathologic mutation in si-Pmel 17 support our conclusion that Pmel 17 is encoded at the silver locus.

Amino Acid Sequence↗
PubMed2000

TRIPLES: a database of gene function in Saccharomyces cerevisiae.

Using a novel multipurpose mini-transposon, we have generated a collection of defined mutant alleles for the analysis of disruption phenotypes, protein localization, and gene expression in Saccharomyces cerevisiae. To catalog this unique data set, we have developed TRIPLES, a Web-accessible database of TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces. Encompassing over 250 000 data points, TRIPLES provides convenient access to information from nearly 7800 transposon-mutagenized yeast strains; within TRIPLES, complete data reports of each strain may be viewed in table format, or if desired, downloaded as tab-delimited text files. Each report contains external links to corresponding entries within the Saccharomyces Genome Database and International Nucleic Acid Sequence Data Library (GenBank). Unlike other yeast databases, TRIPLES also provides on-line order forms linked to each clone report; users may immediately request any desired strain free-of-charge by submitting a completed form. In addition to presenting a wealth of information for over 2300 open reading frames, TRIPLES constitutes an important medium for the distribution of useful reagents throughout the yeast scientific community. Maintained by the Yale Genome Analysis Center, TRIPLES may be accessed at http://ycmi.med.yale.edu/ygac/triples.htm

DNA Transposable Elements↗
PubMed1989

Structure of cDNA coding for rat platelet phospholipase A2.

Three cDNA clones coding for rat platelet phospholipase A2 and a homologous protein were isolated from a rat megakaryocyte cDNA library and sequenced. One (prPLA2-1) carries a 708 nucleotide long insert. The others (prPLA2-2 and -3) differ from clone 1 in three nucleotides and have a 748 nucleotide long insert. All contain a single open reading frame which encodes a 146 amino acid long polypeptide. Based on the deduced amino acid sequence, we concluded that prPLA2-1 encodes rat platelet phospholipase A2. prPLA2-2 and -3 most probably encode a protein homologous to phospholipase A2 with two amino acid replacements. A typical signal peptide sequence (21 amino acid long), located at the NH2 termini of the deduced structure, was immediately followed by a polypeptide which corresponds to the mature enzyme, suggesting that the rat platelet enzyme is not expressed as a proenzyme form. Northern blot analysis showed a single transcript, which is 900 to 1,100 nucleotides long, in the poly(A)+RNA fractions of rat megakaryocytes, bone marrow cells, peritoneal cells of caseinate-treated rats, and spleen cells.

Amino Acid Sequence↗
PubMed1991

Presence of two transcribed malate synthase genes in an n-alkane-utilizing yeast, Candida tropicalis.

The presence of two genomic DNA regions encoding malate synthase (MS) was shown by Southern blot analysis of the genomic DNA from an n-alkane-assimilating yeast, Candida tropicalis, using a partial MS cDNA probe, in accordance with the fact that two types of partial MS cDNAs have previously been isolated. This was also confirmed by the restriction mapping of the two genes screened from the yeast lambda EMBL library. Nucleotide sequence analysis of the respective genomic DNAs, named MS-1 gene and MS-2 gene, revealed that both regions encoding MS had the same length of 1,653 base pairs, corresponding to 551 amino acids (molecular mass of MS-1, 62,448 Da; MS-2, 62,421 Da). Although 29 nucleotide pairs differed in the sequences of the coding regions, the number of amino acid replacements was only one: 159Asn (MS-1)----159Ser (MS-2). In the 5'-flanking regions, there were replacements of four nucleotide pairs, deletion of one pair, and insertion of four pairs. In spite of the fact that two genomic genes were present and transcribed, RNA blot analysis demonstrated that only one band (about 2 kb) was observable even when the carbon sources in the cultivation medium were changed. A comparison of the amino acid sequences was made with MSs of rape (Brassica napus L.), cucumber seed, pumpkin seed, Escherichia coli, and Hansenula polymorpha. A high homology was observed among these enzymes, the results indicating that the protein structure was relatively well conserved through the evolution of the molecule.(ABSTRACT TRUNCATED AT 250 WORDS)

Alkanes↗
PubMedDate not supplied

Paternity exclusion in koalas using hypervariable microsatellites.

Koala microsatellite loci containing the dinucleotide motif (CA)n were isolated from a size-fractionated (250-500 bp) koala genomic library and sequenced. Six locus-specific primer pairs were designed and synthesized for DNA amplification using the polymerase chain reaction (PCR). Microsatellite genotyping of 12 individuals generated unique "fingerprints" for each koala. All six microsatellite loci were polymorphic, with a mean of 6.5 +/- 0.6 alleles/locus. This level of allelic diversity is capable of generating > 4 x 10(9) DNA profiles, making it the most powerful technology for fingerprinting koalas currently available. Observed heterozygosities (H(o)) in the eight unrelated individuals surveyed ranged from 0.25 to 0.75, with a mean of 0.54 +/- 0.06. Mendelian inheritance of the observed polymorphism was confirmed by family studies. We demonstrate that microsatellite loci are ideal genetic markers for paternity exclusion and pedigree analysis of koalas, which have shown little genetic variation using most other methods.

Animals↗
PubMed1998

The modular structure and function of the wheat H1 promoter with S phase-specific activity.

Two histone H1 genes, TH315 and TH325, were isolated from a wheat genomic library. Nucleotide sequence analysis and comparison with other histone gene promoters revealed that the promoters of both genes contain many characteristic motifs conserved among plant histone H1 genes. They are 6 novel short stretches, named CS1 to CS6, and already documented elements or their relatives such as Oct, Oct-like (OLS), Nona-like (NonaLS), CCAAT box, and TATA box. Transient expression experiments with the TH315 promoter/GUS chimeric gene and its mutagenized derivatives showed that two Oct motifs, OLS, and CCAAT box are positive cis-acting elements. NonaLS and CS4 were suggested to be positive cis-acting elements and CS5 and CS6 to be negative elements. An Oct motif and CCAAT box constitutes a type III element and the 202-bp sequence containing these elements from -128 to +74 of the TH315 gene was shown to be sufficient to confer S phase-specific expression. The type III element is found in all plant histone H1 and H2B genes, suggesting that it is a subtype-specific element. Most plant histone genes have one of the type I, II, and III elements. We propose to classify the plant histone genes into three classes, based on the context of Oct in the promoters.

Amino Acid Sequence↗
PubMed1999

Identification and expression of cotton (Gossypium hirsutum L.) plastidial carbonic anhydrase.

Four carbonic anhydrase (CA) cDNA clones were isolated from a 48 h dark-grown cotton (Gossypium hirsutum L.) seedling cDNA library. Nucleotide sequence analysis revealed two different CA isoforms designated GhCA1 and GhCA2. The encoded polypeptides possess N-terminal serine/threonine-rich regions indicative of plastid transit peptides, and approximately 80% sequence identity to other plant plastidial beta-CAs. The GhCA1 cDNA encodes a nearly complete preprotein of 323 amino acids with a molecular mass of 34.9 kDa and a predicted mature protein of 224 amino acids with a molecular mass of 24.3 kDa. Eleven nucleotide differences within ORFs of GhCA1 and GhCA2 result in 5 conservative amino acid substitutions. The 3' GhCA2 untranslated region contains five additional substitutions and one single nucleotide addition. GhCA1 clones, nearly full-length or with 70% of the transit peptide deleted, were expressed as LacZ alpha fusion proteins in E. coli. Lysates of these strains contained 9-fold higher levels of CA activity as compared to untransformed controls and this activity was inhibited by CA-specific inhibitors. Sulfanilamide, acetazolamide, ethoxyzolamide, each at 10 mM, inhibited recombinant CA activity approximately 50%, 65%, and 75%, respectively. In plant tissue homogenates these inhibitors reduced CA activity by 50%, 70%, and 95%, respectively. Although CA activity was bighest in extracts of mature cotton leaves, probing total RNA with GhCA1 revealed CA transcript levels to be highest in the cotyledons of dark-grown cotton seedlings. Collectively, our data indicate the presence of a plastid-localized CA in cotyledons of germinated seeds, suggesting a role for CA in postgerminative growth.

Amino Acid Sequence↗
PubMed2005

Cloning and expression of the genes associated with lipid metabolism in Tsaiya ducks.

Sterol regulatory element binding protein 1 (SREBP1) drives the expression of several lipogenic genes, whereas SREBP2 dictates the expression of every gene involved in cholesterolgenesis in mammals. In the current study, we cloned the cDNA fragments for SREBP1, SREBP2, fatty acid synthase (FAS), 3-hydroxy-3-methylglutaryl-CoA reductase (HMG-CoA reductase), and very low density apolipoprotein-II (apoVLDL-II), the genes associated with lipid metabolism. Fifteen ducks immediately before the first egg was laid (18 wk old) and 15 ducks from the same population at an egg production rate of 80% were killed. Total RNA was extracted from liver and used to amplify the targeted genes by reverse transcription-PCR and screening of a cDNA library. The sequence data showed that Tsaiya duck SREBP1, SREBP2, FAS, and HMG-CoA reductase were highly homologous to that of chicken. Tsaiya duck SREBP1 mRNA was expressed in adipose tissue, cardiac muscle, skeletal muscle, liver, and ovary. The SREBP2 mRNA concentration was highest in liver and ovary. Concentrations of FAS and HMG-CoA reductase mRNA were high in liver and lower in other tissues. The apoVLDL-II mRNA was specifically expressed in the liver. The differences between mRNA concentrations of SREBP1, SREBP2, and FAS in the livers of laying and prelay ducks were not significant. However, the concentrations of hepatic HMG-CoA reductase and apoVLDL-II mRNA were higher in the laying ducks than in prelay ducks. Therefore, laying may affect particular aspects of lipid metabolism, especially biochemical pathways that involved apoVLDL-II and HMG-CoA reductase.

Adipose Tissue↗