In prokaryotes, the promoter region has two short sequences at -10 and -35 positions upstream from the transcription start site. The sequence at -10 is called the Pribnow box, or the -10 element, and has the six nucleotides such as TATAAT whose presence allows a very high transcription rate.
Promoters are an essential part of expression vectors because they control the binding of RNA polymerase to DNA. RNA polymerase transcribes DNA to mRNA which is ultimately translated into a functional protein. Thus the promoter region controls when and where in the organism our gene of interest is expressed.
One of the distinctive features in prokaryotic promoter prediction is the determination of operon structures, because genes within an operon share a common promoter present upstream of the first gene of the operon. Thus, operon prediction is the pace step in prokaryotic promoter prediction. Once an operon structure is known, only the first gene is predicted for the presence of a promoter and regulatory elements, whereas other genes in the operon do not have such DNA elements. There are a lot of methods present for prokaryotic operon prediction. The most accurate and reliable is a set of simple rules. This method depends on two kinds of information, gene orientation and intergenic distances of a pair of genes of interest and conserved linkage of the genes based on comparative genomic analysis. A scoring scheme is made to give operons with different levels of confidence. This method is declared to produce accurate identification of an operon structure, which in turn facilitates the promoter prediction. This newly made scoring approach is, however, not yet available as a computer program. The prediction can be done manually using the rules, however.
BPROM is a web-based program for prediction of bacterial promoters. It uses a linear discriminant function combined with signal and content information such as consensus promoter sequence and oligonucleotide composition of the promoter sites. This program first detects a given sequence for bacterial operon structures by using an intergenic distance of 100 bp as basis for differentiating genes to be in an operon. Once the operons are assigned, the program is able to predict putative promoter sequences. Because most bacterial promoters are present within 200 bp of the protein coding region, the program is most effectively used when about 200 bp of upstream sequence of the first gene of an operon is supplied as input to increase specificity.
FindTerm is a program for searching bacterial ρ-independent termination signals present at the end of operons. It is available from the same site as FGENES and BPROM. The predictions are made based on matching of known profiles of the termination signals combined with energy calculations for the derived RNA secondary structures for the putative hairpin-loop structure. The sequence region that has best scores in features and energy terms is chosen as the prediction. This information can sometimes be useful in defining an operon.