Prime is a rank of highest distinction in many Transformers continuities. Typically, it is used as the identification for the leader of the Autobots, something that is bestowed only on those that carry the Matrix of Leadership within them. It is retroactively derived from Primus, the creator of the Transformers.
With the retcon that Primus is one singular entity that exists (and must exist) threaded through all Transformer continuities, the term Prime is likewise given one singular origin. It was, first of all, the designation granted by Primus to seven of the Thirteen original Transformers created, by his own hand, at the dawn of the physical universe to crew his planetary form.