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Biomedical subjects

C G Simpson

Publications and source records attributed to C G Simpson.

At least 19 recordsLinked to original sources
PubMed2002

Complexities in ETS-domain transcription factor function and regulation: lessons from the TCF (ternary complex factor) subfamily. The Colworth Medal Lecture.

The ETS-domain transcription factor family can be divided into a series of subfamilies. Elk-1 represents the founding member of the ternary complex factor (TCF) subfamily. By focusing on the TCF subfamily, we can demonstrate the complexities that exist in the function and regulation of ETS-domain transcription factors. This article focuses on Elk-1 in detail and summarizes the functions of other TCFs. The key themes covered include the domain structure of the TCFs, the mechanisms of complex formation with serum response factor, regulation of TCFs by mitogen-activated protein kinase cascades, and transcriptional regulatory properties of the TCFs. Finally, the emerging role of the TCFs in vivo is discussed. A picture is developing indicating that, while these proteins exhibit significant sequence and functional conservation, key differences in their structure and regulation are being identified which may relate to unique functions of these proteins in vivo.

Amino Acid Sequence↗
PubMed2001

Expression of intron-containing GUS constructs is reduced due to activation of a cryptic 5' splice site.

An intron-containing beta-glucuronidase (GUS) gene has been used widely in promoter analyses and as a plant transformation marker. Maximal plant gene expression requires accurate and efficient removal of the intron from the expressed pre-mRNA transcripts by splicing. Detailed analysis of splicing of potato ST-LS1 and pea legumin introns from GUS constructs revealed the activation of a cryptic 5' splice site in the GUS coding sequence 4 nt upstream from the authentic intron 5' splice site. About 40% of transcripts utilised the cryptic 5' splice site in tobacco protoplasts, reducing the translational potential of expressed pre-mRNA. The same cryptic splicing event was evident in transgenic tobacco leaves but at reduced levels. Mutations that removed the cryptic 5' splice site are associated with a two-fold enhancement in GUS activity in tobacco protoplasts, highlighting the need for careful examination of introns and their sites of insertion into gene constructs to minimise variability in gene activity and maximise gene expression.

Glucuronidase↗
PubMed2001

Multiple snoRNA gene clusters from Arabidopsis.

Small nucleolar RNAs (snoRNAs) are involved in precursor ribosomal RNA (pre-rRNA) processing and rRNA base modification (2'-O-ribose methylation and pseudouridylation). In all eukaryotes, certain snoRNAs (e.g., U3) are transcribed from classical promoters. In vertebrates, the majority are encoded in introns of protein-coding genes, and are released by exonucleolytic cleavage of linearized intron lariats. In contrast, in maize and yeast, nonintronic snoRNA gene clusters are transcribed as polycistronic pre-snoRNA transcripts from which individual snoRNAs are processed. In this article, 43 clusters of snoRNA genes, an intronic snoRNA, and 10 single genes have been identified by cloning and by computer searches, giving a total of 136 snoRNA gene copies of 71 different snoRNA genes. Of these, 31 represent snoRNA genes novel to plants. A cluster of four U14 snoRNA genes and two clusters containing five different snoRNA genes (U31, snoR4, U33, U51, and snoR5) from Arabidopsis have been isolated and characterized. Of these genes, snoR4 is a novel box C/D snoRNA that has the potential to base pair with the 3' end of 5.8S rRNA and snoR5 is a box H/ACA snoRNA gene. In addition, 42 putative sites of 2'-O-ribose methylation in plant 5.8S, 18S, and 25S rRNAs have been mapped by primer extension analysis, including eight sites novel to plant rRNAs. The results clearly show that, in plants, the most common gene organization is polycistronic and that over a third of predicted and mapped methylation sites are novel to plant rRNAs. The variation in this organization among gene clusters highlights mechanisms of snoRNA evolution.

Arabidopsis↗
PubMed2000

Requirements for mini-exon inclusion in potato invertase mRNAs provides evidence for exon-scanning interactions in plants.

Invertases are responsible for the breakdown of sucrose to fructose and glucose. In all but one plant invertase gene, the second exon is only 9 nt in length and encodes three amino acids of a five-amino-acid sequence that is highly conserved in all invertases of plant origin. Sequences responsible for normal splicing (inclusion) of exon 2 have been investigated in vivo using the potato invertase, invGF gene. The upstream intron 1 is required for inclusion whereas the downstream intron 2 is not. Mutations within intron 1 have identified two sequence elements that are needed for inclusion: a putative branchpoint sequence and an adjacent U-rich region. Both are recognized plant intron splicing signals. The branchpoint sequence lies further upstream from the 3' splice site of intron 1 than is normally seen in plant introns. All dicotyledonous plant invertase genes contain this arrangement of sequence elements: a distal branchpoint sequence and adjacent, downstream U-rich region. Intron 1 sequences upstream of the branchpoint and sequences in exons 1, 2, or 3 do not determine inclusion, suggesting that intron or exon splicing enhancer elements seen in vertebrate mini-exon systems are absent. In addition, mutation of the 3' and 5' splice sites flanking the mini-exon cause skipping of the mini-exon, suggesting that both splice sites are required. The branchpoint/U-rich sequence is able to promote splicing of mini-exons of 6, 3, and 1 nt in length and of a chicken cTNT mini-exon of 6 nt. These sequence elements therefore act as a splicing enhancer and appear to function via interactions between factors bound at the branchpoint/U-rich region and at the 5' splice site of intron 2, activating removal of this intron followed by removal of intron 1. This first example of splicing of a plant mini-exon to be analyzed demonstrates that particular arrangement of standard plant intron splicing signals can drive constitutive splicing of a mini-exon.

Base Sequence↗
PubMed1998

Processing of vertebrate box C/D small nucleolar RNAs in plant cells.

The recent isolation of a number of plant box C/D small nucleolar (sno)RNAs demonstrates the conservation in plants of sequence and structural elements of processed box C/D snoRNAs. Boxes C and D, and terminal inverted repeats are known to be essential for accumulation and processing in vertebrates and yeast. Processing of vertebrate box C/D snoRNAs was examined by expression of various mouse hsc70 intron 5-U14 constructs in tobacco protoplasts. Full-length U14 and internally deleted U14 accumulated in the plant cells. Human U3 and U8 fragments, consistent with processing to internal box C/C' sequences, also accumulated in the plant cells. The similarity of processing behaviour of the vertebrate box C/D constructs in tobacco protoplasts and Xenopus oocytes suggests the mechanism of processing, involving recognition and association of proteins, is conserved in plants.

Animals↗
PubMed1998

Characterization of exon skipping mutants of the COP1 gene from Arabidopsis.

The removal of introns from pre-mRNA requires accurate recognition and selection of the intron splice sites. Mutations which alter splice site selection and which lead to skipping of specific exons are indicative of intron/exon recognition mechanisms involving an exon definition process. In this paper, three independent mutants to the COP1 gene in Arabidopsis which show exon skipping were identified and the mutations which alter the normal splicing pattern were characterized. The mutation in cop1-1 was a G-->A change 4 nt upstream from the 3' splice site of intron 5, while the mutation in cop1-2 was a G-->A at the first nucleotide of intron 6, abolishing the conserved G within the 5' splice site consensus. The effect of these mutations was skipping of exon 6. The mutation in cop1-8 was G-->A in the final nucleotide of intron 10 abolishing the conserved G within the 3' splice site consensus and leading to skipping of exon 11. The splicing patterns surrounding exons 6 and 11 of COP1 in these three mutant lines of Arabidopsis provide evidence for exon definition mechanisms operating in plant splicing.

Arabidopsis↗
PubMed1997

East meets West: a comparison of eastern block/western aeromedical practices.

Under the auspices of the European Command (EUCOM) Military-to-Military Exchange Program, the authors participated in 13 trips to visit aeromedical facilities of nine Eastern European nations (Albania, Belarus, Bulgaria, Czech Republic, Hungary, Lithuania, Poland, Romania, and Slovakia). In addition, eight of these Eastern European nations visited United States Air Force (USAF) aeromedical facilities. This article highlights the similarities and differences noted between the USAF and Eastern Europe in the practice of aerospace medicine. Flight surgeons from both Eastern Europe and the USAF address issues such as physiologic stresses of flight (acceleration, hypoxia, etc.) and lifestyle stresses (rest, diet, alcohol, cigarettes, etc.). Eastern European Flight Surgeons do not regularly fly. The Eastern European approach to medical standards and screening for aviation applicants is much stricter and more comprehensive than ours. Several of the nations visited had active research programs at their central aeromedical institute emphasizing aircrew selection and retention standards. With the exception of the Czech Republic, Eastern European nations did not routinely grant waivers for chronic medical conditions such as hypertension in aircrew. Soviet-built aircraft had many unique features such as an outside-in attitude indicator and an auto-recovery system.

Aerospace Medicine↗
PubMed1996

Arabidopsis consensus intron sequences.

We have analysed 998 Arabidopsis intron sequences in the EMBL database. All Arabidopsis introns to adhere to the :GU ... AG: rule with the exception of 1% of introns with :GC at their 5' ends. Virtually all of the introns contained a putative branchpoint sequence (YUNAN) 18 to 60 nt upstream of the 3' splice site. Although a polypyrimidine tract was much less apparent than in vertebrate introns, the most common nucleotide in the region upstream of the 3' splice site was uridine. Consensus sequences for 5' and 3' splice sites and branchpoint sequences for Arabidopsis introns are presented.

Arabidopsis↗
PubMed1996

Mutation of putative branchpoint consensus sequences in plant introns reduces splicing efficiency.

Intron lariat formation between the 5' end of an intron and a branchpoint adenosine is a fundamental aspect of the first step in animal and yeast nuclear pre-mRNA splicing. Despite similarities in intron sequence requirements and the components of splicing, differences exist between the splicing of plant and vertebrate introns. The identification of AU-rich sequences as major functional elements in plant introns and the demonstration that a branchpoint consensus sequence was not required for splicing have led to the suggestion that the transition from AU-rich intron to GC-rich exon is a major potential signal by which plant pre-mRNA splice sites are recognized. The role of putative branchpoint sequences as an internal signal in plant intron recognition/definition has been re-examined. Single nucleotide mutations in putative branchpoint adenosines contained within CUNAN sequences in four different plant introns all significantly reduced splicing efficiency. These results provide the most direct evidence to date for preferred branchpoint sequences being required for the efficient splicing of at least some plant introns in addition to the important role played by AU sequences in dicot intron recognition. The observed patterns of 3' splice site selection in the introns studied are consistent with the scanning model described for animal intron 3' splice site selection. It is suggested that, despite the clear importance of AU sequences for plant intron splicing, the fundamental processes of splice site selection and splicing in plants are similar to those in animals.

Amylases↗
PubMed1994

Genetic analysis of DNA fingerprints and virulences in Erysiphe graminis f.sp. hordei.

A DNA probe, E9, which has been used extensively in population genetic studies of the barley powdery mildew pathogen, Erysiphe graminis f.sp. hordei, was shown to be homologous to dispersed sequences in the genome of this fungus. In a cross of the isolates CC52 and DH14, fragments with homology to E9 mapped to six clusters of loci. Avirulences matching five resistance genes in barley were controlled by single genes, in accordance with the gene-for-gene hypothesis, while avirulence matching a sixth resistance gene, Mla13, was controlled by two genes. A gene which controls the response to a fungicide, ethirimol, was not linked to any other gene. In all, seven linkage groups, comprising 22 loci, were detected. The results indicate that E9 can be used to identify members of a clone of E.g. f.sp. hordei, but should not be used for quantitative population genetic analysis.

Ascomycota↗