The Histidine Biosynthetic Genes in the Superphylum Bacteroidota-Rhodothermota-Balneolota-Chlorobiota: Insights into the Evolution of Gene Structure and Organization

The Operon as a Conundrum of Gene Dynamics and Biochemical Constraints: What We Have Learned from Histidine Biosynthesis

Operons represent one of the leading strategies of gene organization in prokaryotes, having a crucial influence on the regulation of gene expression and on bacterial chromosome organization. However, there is no consensus yet on why, how, and when operons are formed and conserved, and many different theories have been proposed. Histidine biosynthesis is a highly studied metabolic pathway, and many of the models suggested to explain operons origin and evolution can be applied to the histidine pathway, making this route an attractive model for the study of operon evolution. Indeed, the organization of his genes in operons can be due to a progressive clustering of biosynthetic genes during evolution, coupled with a horizontal transfer of these gene clusters. The necessity of physical interactions among the His enzymes could also have had a role in favoring gene closeness, of particular importance in extreme environmental conditions. In addition, the presence in this pathway of paralogous genes, heterodimeric enzymes and complex regulatory networks also support other operon evolution hypotheses. It is possible that histidine biosynthesis, and in general all bacterial operons, may result from a mixture of several models, being shaped by different forces and mechanisms during evolution.

Proposal to include the categories kingdom and domain in the International Code of Nomenclature of Prokaryotes

Observations made after introduction of the phylum category into the International Code of Nomenclature of Prokaryotes (ICNP) indicate that the addition of a category should usually be conducted before informal names at that rank become widely used. It is thus investigated whether it would be beneficial to add further categories. An extrapolation from the number of names validly published under the ICNP at the distinct principal categories was conducted. This extrapolation indicated that two principal ranks above phylum rank would also harbour validly published names if the according categories were covered by the ICNP. The appropriate categories would be kingdom and domain, regarded as separate principal ranks. The benefit from introducing these ranks is confirmed by analysing the previous taxonomic activity above phylum level and the nomenclatural problems associated with this activity. An etymological examination of the way names of taxa above genus level are formed under distinct codes of nomenclature provides hints for implementing additional categories. According emendations of the ICNP are proposed to include kingdom and domain as a means of further stabilizing prokaryotic nomenclature.