All the structural genes of an operon are turned ON or OFF together, due to a single promoter and operator upstream to them, but sometimes more control over the gene expression is needed. To achieve this aspect, some bacterial genes are located near together, but there is a specific promoter for each of them; this is called gene clustering. Usually these genes encode proteins which will work together in the same pathway, such as a metabolic pathway. Gene clustering helps a prokaryotic cell to produce metabolic enzymes in a correct order.
In one study, it has been posited that in the Asgard (archaea), ribosomal protein coding genes occur in clusters that are less conserved in their organization than in other Archaea; the closer an Asgard (archaea) is to the eukaryotes, the more dispersed is the arrangement of the ribosomal protein coding genes.