Table 1.

Ribonucleases and accessory proteins involved in mRNA decay in Escherichia coli.

RNases/Proteins	Gene	Activity	Known functions
RNase E	rne	Endoribonuclease	mRNA decay, tRNA processing, tRNA maturation, and degradation of rRNA, degradation of sRNAs
RNase G	rng	Endoribonuclease	mRNA decay, rRNA processing
RNase III	rnc	Endoribonuclease	mRNA decay, rRNA processing, sRNA degradation
RNase P	rnpA, rnpB	Endoribonuclease	Separation of pre-tRNAs from polycistronic transcripts, tRNA 5’ end maturation, mRNA decay*
YbeY	ybeY	Endoribonuclease	rRNA maturation
RNase I	rna	Endoribonuclease	Specific function unknown, Located in the periplasmic space
RNase HI	rnhA	Endoribonuclease	DNA replication
RNase HII	rnhB	Endoribonuclease	DNA replication
RNase Z/RNase BN	rbn	Endoribonuclease/3’ → 5’ exoribonuclease	mRNA decay, sRNA degradation, tRNA maturation
PNPase	pnp	3’ → 5’ exoribonuclease	mRNA decay, rRNA degradation, sRNA degradation; Biosynthetic activity adds polynucleotide tails to mRNA decay intermediates
RNase II	rnb	3’ → 5’ exoribonuclease	mRNA decay
RNase R	rnr	3’ → 5’ exoribonuclease	mRNA decay, rRNA maturation and degradation
RNase PH	rph	3’ → 5’ exoribonuclease	tRNA maturation
RNase T	rnt	3’ → 5’ exoribonuclease	tRNA and rRNA maturation
RNase D	rnd	3’ → 5’ exoribonuclease	tRNA maturation
oligoribonuclease	orn	3’ → 5’ exoribonuclease	mRNA decay (oligoribonucleotides 2–5 nt in length)
RNase AM	trpH	5’ → 3’ exoribonuclease	rRNA maturation
Poly(A) polymerase (PAP I)	pcnB	Polyadenylation	Poly(A) tails provides unstructured binding sites for 3’ → 5’ exonucleases. Promotes degradation of full-length transcripts and decay intermediates.
Hfq	hfq	RNA binding protein	Modulation of poly(A) addition, promotes mRNA/sRNA interaction
ProQ	proQ	RNA binding protein	RNA/RNA interaction, inhibition of exonucleolytic decay
CsrA	csrA	RNA binding protein	mRNA stability

^*:Based on RNA-seq analysis of the rnpA49 transcriptome (Mohanty and Kushner, unpublished results).