I cannot for the life of me figure this out. In the following figure, you can find ajuA and AjuA for example.

I do understand that the lower-case ones are the genes. The arrows indicate the direction of transcription. However, what is the difference to the upper-case AjuA? The text speaks of subunits. How are the two related? When do I speak of ajuA and when would I be talking about AjuA?

I would also be happy if you could point me in the direction of some literature about the basics of this kind of notation.

PS: I do understand the mechanisms of the biosynthetic route and am familiar with the different domains in the modules as well as PKS and NRPS modules.

enter image description here


It's just the nomenclature:

Bacteria: Gene symbols are typically composed of three lower-case, italicized letters that serve as an abbreviation of the process or pathway in which the gene product is involved (e.g., rpo genes encode RNA polymerase). To distinguish among different [but related genes], the abbreviation is followed by an upper-case letter (e.g., the rpoB gene encodes the β subunit of RNA polymerase). Protein symbols are not italicized, and the first letter is upper-case (e.g., RpoB).


You can check out the Wikipedia article on Gene Nomenclature for more information.

  • $\begingroup$ But what is the relationship between gene and protein symbols? Can they be used interchangeably? The paper talks about AjuK containing a module, while "genes ajuK and ajuL encode the first two biosynthetic proteins". Does that mean, the gene ajuK for example encodes the protein AjuK, which in turn does biosynthetic stuff? $\endgroup$
    – basseur
    May 24 '18 at 18:12
  • $\begingroup$ @basseur "Does that mean, the gene ajuK for example encodes the protein AjuK, which in turn does biosynthetic stuff?" Without reading the paper, yes that's what it sounds like. $\endgroup$
    – canadianer
    May 24 '18 at 18:41

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