Diana F. Hill

Messenger RNA recognition in Escherichia coli: a possible second site of interaction with 16S ribosomal RNA.

Examination of the nucleotides following the ATG or GTG initiation codons of a file of 251 genes from Escherichia coli has shown that 247 (98.4%) of them contain a sequence of at least three and 168 (66.9%) of them a sequence of at least four consecutive nucleotides that is complementary to some part of the 16 nt at the 5′ terminus of the bacterial 16S rRNA. It is proposed that this sequence, which falls within the first 24 nt coding for the genetic message, might be involved in mRNA recognition through a mechanism analogous to the well‐established ‘Shine–Dalgarno’ interaction with the 3′ terminus of the 16S rRNA. Comparison of these data with data derived from a file of 117 ‘false’ gene starts that have a Shine–Dalgarno‐like sequence followed by a suitably spaced ATG or GTG triplet but which are believed not to lie at the beginnings of genetic messages shows the association that we have found to be statistically significant at the 99.9% level.

The isolation and characterisation of a cDNA clone encoding L-asparaginase from developing seeds of lupin (Lupinus arboreus)

An L-asparaginase cDNA clone, BR4, was isolated from a Lupinus arboreus Sims developing seed expression library by screening with polyclonal antibodies to the seed asparaginase. The cDNA hybridised with an oligonucleotide probe designed from amino acid sequence data and was found on sequencing to be 947 bp in length. Six polypeptide sequences obtained previously could be placed along the longest open reading frame. Computer-aided codon use analysis revealed that the cDNA sequence was consistent with other plant genes in terms of codon use. The cDNA insert was used to analyse asparaginase transcription in various tissues by northern blot analysis. A transcript size of approximately 1.2 kb was detected in L. arboreus seed total and poly(A)+ RNA. The level of this transcript declined from 30 days after anthesis to an undetectable level by day 55. Furthermore, under the high stringency conditions used, the seed asparaginase cDNA did not hybridise with total or poly(A)+ RNA isolated from root tips, suggesting that the asparaginase known to be present in this tissue may be the product of a different gene. Southern analysis suggested the seed asparaginase is a single-copy gene. The plant asparaginase amino acid sequence did not have any significant homology with microbial asparaginases but was 23% identical and 66% similar (allowing for conservative substitutions) to a human glycosylasparaginase.

Sequence analysis of the inverted terminal repetition in the genome of the parapoxvirus orf virus

Two BamHI fragments from the right-hand terminal region of the orf virus genome have been sequenced. The bulk of the inverted terminal repetition (ITR) sequence is contained within these fragments and makes up 3388 bp of the 4425-bp sequence reported. The overall base composition of the larger sequence is 59.4% G + C and of the ITR, 60.2% G + C. An extremely G/C-rich (83.2%) block of sequence was found spanning the ITR/unique sequence junction. The bulk of the ITR could be divided into three blocks of directly repeated sequences. One block begins about 250 nucleotides from the terminus and is a direct repeat 15 bp long, repeated 14 times. The other blocks contain seven sequence sets ranging from 16 to 36 nucleotides which are repeated 2 to 4 times, interspersed with one another, interrelated in sequence, and sometimes separated by unique sequence. Eight open reading frames (ORFs), each with the potential to code for polypeptides of 50 residues or more, were identified. Three were found within the ITR, four spanned the ITR/unique sequence junction and one was found outside the ITR. A search for putative poxvirus transcriptional control signals indicated that three of the eight ORFs are likely to be transcribed early, all in the same direction toward the right end of the genome. Sequences of the type T(A)3-5T were found only twice in the sequence and only one preceded an ORF.

Activity expressed from cloned Anacystis nidulans large and small subunit ribulose bisphosphate carboxylase genes.

SummaryThe ribulose bisphosphate carboxylase/oxygenase (EC4.1.1.39) (RubisCO) large and small subunit genes from Anacystis nidulans have been cloned as a single fragment into M 13mp10 and pEMBL8 and expressed in Escherichia coli. From M 13mp10 a low yield of enzyme with high specific activity was obtained. The molecular weight of the active enzyme was 260 000 Da and of the inactive enzyme approximately 730 000 Da. The small and large subunits cloned separately did not express activity. The RubisCO gene cloned into pEMBL8 expressed activity up to 22 times that from the M 13 cloned RubisCO DNA. The RubisCO protein produced by the pEMBL cloned gene had a normal MW (550 000). Immunoprecipitation and polyacrylamide gel electrophoresis showed the presence of both large and small subunits.

Isolation of chromosome-specific paints from high-resolution flow karyotypes of the sheep (Ovis aries)

High-resolution bivariate flow karyotypes were obtained using fibroblast cell lines from a sheep with a normal karyotype (2n=54), from sheep carrying Robertsonian translocation chromosomes and from sheep—hamster somatic cell hybrids. By taking advantage of the presence of chromosome polymorphisms, translocation chromosomesand sheep—hamster somatic cell hybrids, all sheep chromosomes were isolated by flow sorting. Chromosome-specific paints were generated from each sorted peak using degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR). The sheep chromosome present in each peak was identified by chromosome-specific microsatellite analysis of the DOP-PCR products and fluorescence in situ hybridization (FISH) onto DAPI-banded sheep metaphase chromosomes. The chromosome-specific DNA obtained in this study can be used for the production of genomic libraries and as a resource for mapping randomly cloned DNA sequences that will greatly aid the construction of genetic and physical maps in the sheep. The chromosome-specific paints will facilitate chromosome identification and contribute to the study of karyotype evolution in the sheep and related species.

The DNA-binding protein of Pf1 filamentous bacteriophage: amino-acid sequence and structure of the gene.

The amino‐acid sequence of the single‐stranded DNA‐binding protein of bacteriophage Pf1 and the nucleotide sequence of the corresponding gene have been determined. The protein has 144 amino acids and a molecular weight of 15 400; the gene consists of 435 nucleotides. The amino‐acid sequence was determined by Edman degradation, carboxypeptidase A, B, and P digestion of intact protein and of peptides derived by chymotrypsin, Staphylococcus aureus V8 protease, and trypsin digestion. The nucleotide sequence was determined by the dideoxy method after random cloning of fragments of Pf1 DNA into M13. No sequence homology could be established between the amino‐acid sequence of the DNA‐binding protein of Pseudomonas aeruginosa‐specific bacteriophage Pf1 and bacteriophage fd of Escherichia coli.

An ovine CFTR variant as a putative cystic fibrosis causing mutation.

This report describes a DNA variant in the ovine cystic fibrosis transmembrane conductance regulator (CFTR) gene that has been previously reported as a putative cystic fibrosis causing mutation in humans. The variant is a guanine to adenine base change at position 1019 of the ovine CFTR cDNA, corresponding to an arginine (R) to glutamine (Q) amino acid substitution at position 297 in the predicted CFTR polypeptide. The equivalent R297Q mutation in exon 7 of the human CFTR gene has been reported in a CF patient. This is the first putative cystic fibrosis mutation to be detected in another animal species.

The isolation and characterization of a cDNA clone encoding Lupinus angustifolius root nodule glutamine synthetase

Glutamine synthetase, purified from Lupinus angustifolius legume nodules, was carboxymethylated and succinylated prior to chemical or enzymatic cleavage. Peptides were purified and sequenced. An oligonucleotide probe was constructed for the sequence MPGQW. This probe was used to identify a glutamine synthetase cDNA clone, pGS5, from a lupin nodule cDNA library constructed in pBR322. pGS5 was sequenced (1043 bp) and computer-assisted homology searching revealed a high degree of conservation between this lupin partial cDNA clone and other plant glutamine synthetases at both the amino acid (>90%) and nucleotide (>80%) level. Northern and Southern analyses using pGS5 supported the conclusion that a multigene glutamine synthetase family exists in lupin which is differentially expressed in both an organ-specific and temporal manner. Western and Northern blot analyses indicated the accumulation of a glutamine synthetase specific mRNA species during nodule development corresponded to the appearance of a novel glutamine synthetase polypeptide between 8 and 10 days after rhizobial inoculation.

Genetic variation within the ovine cystic fibrosis transmembrane conductance regulator gene.

We report here the results of a preliminary screening programme to identify natural mutations in the ovine cystic fibrosis transmembrane conductance regulator (CFTR) gene. Nine regions of the ovine CFTR gene were screened, corresponding to human CFTR gene exons 4, 6b, 7, 9, 10, 11, 12, 17b and 20. DNA samples from up to 2000 individual sheep were examined by single-stranded conformation polymorphism (SSCP) of each exon. In addition to the mutation (R297Q) reported previously, we have found several interesting variants, including intronic DNA variants and exonic polymorphisms.

Isolation and characterisation of DNA from whale bone

DNA was extracted from a sperm whale rib bone, and an ear bone from an unidentified large baleen whale. Prior to extraction the two bones had been subjected to various environmental conditions resulting in limited decomposition of the bone material. Specific mitochondria! DNA sequences were amplified from the extracts using the technique of polymerase chain reaction. Subsequent sequencing of these products confirmed that the rib bone was indeed from a sperm whale, and that the ear bone was from a blue whale. The results show that genetic information can be obtained from whale bones that have been exposed to the elements.