Table 2.

Studied enzymes with detectable RNA binding.

Protein	Description of Enriched RNA Features	Predicted RNA Secondary Structure a
pyruvate kinase (PykF)	various mRNAs/asRNAs with no apparent communal attribute	-
phosphoglycerate kinase (Pgk)	poorly defined hairpins, showing A-rich loops of variable length as common feature
glyceraldehyde-3-phosphate dehydrogenase (GapA)	poorly defined, AU-rich sequence stretches
thymidylate synthase (ThyA)	hairpin with strictly conserved sequence GC(AGA)GU (brackets indicating triloop)
aconitase (AcnB)	poorly defined stem-loops with 3′-adjacent U-rich stretches
glutamate-5-kinase (ProB)	small number of specific fragments (two mRNAs and one asRNA)	-
quinone oxidoreductase (QorA)	few specific mRNAs/asRNAs with a potential motif (see Figure 8A). top-scoring: yffO mRNA fragment.
positive control MS2 phage coat protein	bacteriophage operator hairpin-like motif NANN(ANCA)N′N′N′ (N and N′ indicate complementary bases, brackets indicate loop)

^a manually curated structures based on different predictions, see Section 4.