It was observed that the genes apparently regulated by MAEB generally have a role in primary metabolism, i.e., the synthesis, catabolism or transport of small molecules; few MAEB-associated genes are involved in other functions, such as signal transduction, motility or replication.
If the MAEB motif is really a short DNA-binding domain and its reverse complement, then the 3' part of the apparent RNA stem at this position should contain the complementary pyrimidine, and not also be a purine.
Although the repetitive nature of MAEB stem-loops supports this kind of a role, the association of MAEB with metabolic genes is inconsistent with known repetitive elements, which are typically the result of selfish replication or errors in replication.
The third hypothesis advanced is that MAEB stem-loops bind a protein, and the multiple occurrences of MAEB stem-loops within a single RNA molecule would allow the binding of more proteins per RNA molecule.
Such an arrangement is similar to CsrB RNA, which contains roughly 18 hairpins, each of which binds one CsrA protein subunit.