The NRSub database: update 1997

Differential display approach to quantitation of environmental stimuli on bacterial gene expression

The differential display of the mRNA technique for eukaryotes is fruitful in identifying genes with altered transcription rates caused by exogenous or endogenous stimuli. Prokaryotic analogues of the method using arbitrary oligonucleotides may reach a complete statistical genome coverage. Thus a genome-wide mass screening for transcriptionally regulated sequences will be possible. However, the primer sets have to be optimized for a given species to result in maximum band yields. Hence the construction of primers requires the calculation of oligonucleotide frequency distributions from known coding regions to choose sequences with frequent occurrence in the bacterial genome. After completion of many whole genome sequencing projects, differentially regulated cDNA sequences are readily identified by sequence comparisons.

Recent developments in biological sequence databases

Biological sequence databases are currently being re-engineered to make them more efficient and easier to use. This re-engineering is also providing an infrastructure to make it easier to interrogate and integrate data from different sources. The net result of this effort should be a great improvement in the power and availability of bioinformatics resources to the general biology community.

Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species

The amino-acid composition of 23,490 proteins from 59 bacterial species was analyzed as a function of genomic G+C content. Observed amino-acid frequencies were compared with those expected from a neutral model assuming the absence of selection on average protein composition. Integral membrane proteins and non-integral membrane proteins were analyzed separately. The average deviation from this neutral model shows that there is a selective pressure increasing content in charged amino acids for non-integral membrane proteins, and content in hydrophobic amino acids for integral membrane proteins. Amino-acid frequencies were greatly influenced by genomic G+C content, but the influence was found to be often weaker than predicted. This may be evidence for a selective pressure, maintaining most amino-acid frequencies close to an optimal value. Concordance between the genetic code and protein composition is discussed in the light of this observation.