Dennis M. Burns

Rare codons in E. coli and S. typhimurium signal sequences

Codon usage has been examined in the signal sequences of 27 genes encoding proteins which possess leader peptides, and are inner‐membrane located or exported. The results have been compared with codon usage in the corresponding coding sequences of most of the mature proteins. A bias is observed in the usage of rare codons for two of the three hydrophobic amino acids for which there are rare codons. Since hydrophobic residues are predominant in leader peptides, we suggest that a resulting concentration of rare codons in the signal sequence may play a role (or have played a role in the evolutionary past) in the secretion process by delaying translation.

Recovery of genomic DNA from archived PCR product mixes for subsequent multiplex amplification and typing of additional loci: forensic significance for older unsolved criminal cases

A method for genomic DNA recovery from different types of PCR product mixes suitable for multiplex amplification and typing using the Profiler Plus STR typing system has been investigated. The application of this method is of significance in cases where the original DNA samples have been exhausted due to repeated typing analyses in an effort to maximize their evidentiary value. Such cases typically involve samples analyzed using the available DNA typing systems of the time which gave a markedly lower power of discrimination, either alone or in combination, compared to that of modern multiplex STR typing systems. It was found that an effective method for recovering genomic DNA from HLA-DQA1 +PM and CTT triplex amplification mixes, suitable for reproducible achievement of the complete Profiler Plus profile, involved the use of Amicon Microcon-100 microconcentrators. Interestingly, this method was not required to achieve the complete nine STR profile using D1S80 amplification mixes.

The role of the intracellular inhibitor of periplasmic UDP-sugar hydrolase (5'-nucleotidase) in Escherichia coli: cytoplasmic localisation of 5'-nucleotidase is conditionally lethal.

E. coli UshA, a bifunctional enzyme with UDP‐sugar hydrolase and 5′‐nucleotidase activities, is secreted to the periplasm but has a specific protein inhibitor located in the cytoplasm. It has been previously suggested that some 5′‐nucleotidase, or a folded domain of this enzyme, may be active in the cytoplasm prior to export. If true, the intracellular inhibitor may have a role in protecting the cell from the likely deleterious effects of any intracellular UshA activity. Using deletion mutagenesis to remove the UshA signal peptide, we have shown that the resulting UshA derivative is an active cytoplasmic 5′‐nucleotidase, and causes conditional lethality. Our results support the hypothesis that the physiological role of the UshA inhibitor is to protect the intracellular nucleotide pool from any cytoplasmic 5′‐nucleotidase activity.