Rita E. Godfrey

Transcriptomic responses of European flounder (Platichthys flesus) to model toxicants

The temporal transcriptomic responses in liver of Platichthys flesus to model environmental pollutants were studied over a 16-day time span after intraperitoneal injection with cadmium chloride (50 microg/kg in saline), 3-methylcholanthrene (25 mg/kg in olive oil), Aroclor 1254 (50 mg/kg in olive oil), tert-butyl-hydroperoxide (5 mg/kg in saline), Lindane (25mg/kg in olive oil), perfluoro-octanoic acid (100 mg/kg in olive oil) and their vehicles, olive oil (1 ml/kg) or saline (0.9%). Statistical, gene ontology and supervised analysis clearly demonstrated the progression from acute effects, biological responses to and recovery from the treatments. Key biological processes disturbed by the individual treatments were characterised by gene ontology analyses and individual toxicant-responsive genes and pathways were identified by supervised analyses. Responses to the polyaromatic and chlorinated aromatic compounds showed a degree of commonality but were distinguishable and they were clearly segregated from the responses to the pro-oxidants cadmium and the organic hydroperoxide, as well as from the peroxisomal proliferator, perfluoro-octanoic acid. This study demonstrated the utility of the microarray technique in the identification of toxicant-responsive genes and in discrimination between modes of toxicant action.

Transcription of the plasmid-encoded toxin gene from Enteroaggregative Escherichia coli is regulated by a novel co-activation mechanism involving CRP and Fis

Enteroaggregative Escherichia coli (EAEC) is a major cause of diarrhoea in developing countries. EAEC 042 is the prototypical strain. EAEC 042 secretes the functionally well‐characterized Pet autotransporter toxin that contributes to virulence through its cytotoxic effects on intestinal epithelial cells. Following a global transposon mutagenesis screen of EAEC 042, the transcription factors, CRP and Fis, were identified as essential for transcription of the pet gene. Using both in vivo and in vitro techniques, we show that the pet promoter is co‐dependent on CRP and Fis. We present a novel co‐activation mechanism whereby CRP is placed at a non‐optimal position for transcription initiation, creating dependence on Fis for full activation of pet. This study complements previous findings that establish Fis as a key virulence regulator in EAEC 042.

Identification and characterization of inositol 1,4,5-trisphosphate receptors in rat testis

PCR analysis and immunoblotting with isoform specific antibodies was used to identify the presence of type I, II and III inositol 1,4,5-trisphosphate receptors (InsP3Rs) in rat testis. PCR analysis also revealed that rat testis express both forms of the S1 splice variant (S1+ and S1-), but only the S2- from of the S2 splice variant of the type I InsP3 receptor. PCR analysis was also used to identify InsP3R isoform expression at a cellular level using myoid, Sertoli and germ cells derived from the testis of Wistar rats. The extent of [3H]-InsP3 binding was found to be 9 times lower for testicular microsomes than for cerebellar microsomes, with a Bmax of 1.4 pmoles/mg protein compared to 12.5 pmoles/mg protein for cerebellar microsomes. The Kd for InsP3 binding to its receptor in testicular microsomes was 60 +/- 10 nM which was similar to that found for cerebellar microsomes (80 +/- 20 nM). InsP3-induced Ca2+ release (IICR) in testicular microsomes was found to have an EC50 (concentration which causes a half-maximal response) of 0.5 +/- 0.03 microM, also similar to that seen for cerebellar microsomes (0.3 microM). Maximal IICR occurred at about 20 microM InsP3, with up to 4% of total intracellular Ca2+ stores being mobilized as compared to between 10-30% for cerebellar microsomes. Time resolved IICR using stopped-flow spectrofluorimetry, showed the kinetics of IICR for this testis preparation to be monophasic with a maximum rate constant of 0.15 s-1 at 30 microM InsP3. The rate constants are 7 times slower than values for cerebellar microsomes under similar conditions (approximately 1 s-1) and taken together with the binding data support the proposal that the receptor density/Ca2+ store is approximately 8 times lower than seen in cerebellar microsomal vesicles. The pharmacological properties as assessed using heparin and InsP3 analogues also confirmed similar behaviour for testicular InsP3Rs and cerebellar InsP3Rs.

Transcription initiation in the Escherichia coli K-12 malI^malX intergenic region and the role of the cyclic AMP receptor protein

The Escherichia coli K-12 malI-malX intergenic region contains two divergent promoters, which have been investigated by both mutational and biochemical analysis. The malX promoter drives transcription initiation from a location that is 43 bp upstream from the malX translation start codon. Expression from the malX promoter is dependent on binding of the cyclic AMP receptor protein (CRP) to a DNA site centred 41.5 bp upstream of the transcript start. The malI promoter drives transcription initiation from a location 85 bp upstream from the malX transcript start and it is active without the CRP. Expression from the malI promoter can be stimulated by the CRP. Mutational analysis suggests that the malI promoter has an unusual organization.

Characterisation of the connexin32 promoter and changes in response element complexes in rat liver and hepatocytes during culture associated with oxidative stress

Hepatic gap junctional intercellular communication (GJIC), mediated principally by connexin 32, provides a mechanism for regulating multicellular activities between neighbouring cells. The control of Cx32 gene expression at the transcriptional level has been investigated in rat liver tissue and in primary rat hepatocytes during culture. Several response elements have been identified and characterised using the electrophoretic mobility shift assay. Nuclear protein extract prepared from rat primary hepatocytes cultured for 2 h gave a larger number of DNA-protein complexes than observed with extracts from liver in vivo, including complexes containing Sp1. In contrast, nuclear extracts prepared from primary rat hepatocytes cultured for 96 h, and subject to oxidative stress, gave altered DNA-protein complexes when compared to those from hepatocytes cultured for 2 h. These results indicate that culture conditions, known to cause a loss of connexin expression, can modulate the transcription of Cx32 in hepatocytes by affecting the regulatory trans/cis-interactions of redox-sensitive zinc finger proteins within the promoter.

Targets for the MalI repressor at the divergent Escherichia coli K-12 malX-malI promoters.

Random mutagenesis has been used to identify the target DNA sites for the MalI repressor at the divergent Escherichia coli K-12 malX-malI promoters. The malX promoter is repressed by MalI binding to a DNA site located from position -24 to position -9, upstream of the malX promoter transcript start. The malI promoter is repressed by MalI binding from position +3 to position +18, downstream of the malI transcript start. MalI binding at the malI promoter target is not required for repression of the malX promoter. Similarly, MalI binding at the malX promoter target is not required for repression of the malI. Although the malX and malI promoters are regulated by a single DNA site for cyclic AMP receptor protein, they function independently and each is repressed by MalI binding to a different independent operator site.

Sequence of ptb1, a Gene for the β subunit of the type-II geranylgeranyltransferase from the fission yeast Schizosaccharomyces pombe

We have isolated and sequenced the ptb1 gene from the fission yeast Schizosaccharomyces pombe. Sequence analysis suggests that Ptb1 is the β subunit of the type‐II geranylgeranyltransferase that is responsible for geranylgeranylation of the Rab‐like YPT proteins in this yeast. The sequence has been deposited in the EMBL data library under the Accession Number X92183.

Regulation of nrf operon expression in pathogenic enteric bacteria: Sequence divergence reveals new regulatory complexity

The Escherichia coli K‐12 nrf operon encodes a periplasmic nitrite reductase, the expression of which is driven from a single promoter, pnrf. Expression from pnrf is activated by the FNR transcription factor in response to anaerobiosis and further increased in response to nitrite by the response regulator proteins, NarL and NarP. FNR‐dependent transcription is suppressed by the binding of two nucleoid associated proteins, IHF and Fis. As Fis levels increase in cells grown in rich medium, the positioning of its binding site, overlapping the promoter −10 element, ensures that pnrf is sharply repressed. Here, we investigate the expression of the nrf operon promoter from various pathogenic enteric bacteria. We show that pnrf from enterohaemorrhagic E. coli is more active than its K‐12 counterpart, exhibits substantial FNR‐independent activity and is insensitive to nutrient quality, due to an improved −10 element. We also demonstrate that the Salmonella enterica serovar Typhimurium core promoter is more active than previously thought, due to differences around the transcription start site, and that its expression is repressed by downstream sequences. We identify the CsrA RNA binding protein as being responsible for this, and show that CsrA differentially regulates the E. coli K‐12 and Salmonella nrf operons.