RNase E: still a wonderfully mysterious enzyme

Abstract

SummaryRibonuclease E (RNase E), which is encoded by an essential Escherichia coli gene known variously as me, ams, and hmp, was discovered initially as an rRNA-processing enzyme but is now known to have a general role in RNA decay. Multiple functions, including the ability t o cleave RNA endonucleolytically in AU-rich single-strand regions, RNA-binding capabilities, and the ability to interact with polynucleotide phosphorylase and other proteins implicated in the processing and degradation of RNA, are encoded by its 1061 amino acid residues. The presence of homologues and functional analogues of the m e gene in a variety of prokaryotic and eukaryotic species suggests that its functions have been highly conserved during evolution. While much has been learned in recent years about the structure and functions of RNase E, there is continuing mystery about possible additional activities and molecular interactions of this enzyme.

A developmentally regulated Streptomyces endoribonuclease resembles ribonuclease E of Escherichia coli

“…approximately 70 kDa), smaller bands likely to represent products of proteolytic degradation were also observed in our preparations of RNase ES. E. coli RNase E is highly susceptible to proteolysis during purification (Carpousis et al, 1994), and this property led to continuing uncertainty about this enzyme's true size until the gene encoding it was eventually isolated and characterized (for reviews, see Ehretsmann et al, 1992;Melefors et al, 1993;Cohen and McDowall, 1997). Thus, we cannot be certain that the 70 kDa peptide is not itself a degradation product of a larger protein.…”

“…RNase E is an E. coli endoribonuclease that has been shown to have a key role in the processing of ribosomal RNA and the degradation of a variety of messenger RNAs; additionally, by its cleavage of RNA I, the antisense repressor of replication of ColE1-type plasmids, RNase E can regulate DNA replication (for reviews, see Ehretsmann et al, 1992;Melefors et al, 1993;Cohen and McDowall, 1997). This enzyme is a 118 kDa, 1061 amino acid protein that cleaves single-stranded regions of RNA site specifically in segments rich in A þ U nucleotides; in E. coli cells, RNase E can form macromolecular complexes with other proteins that assist in, or otherwise affect, RNA decay (for a recent review, see Cohen and McDowall, 1997).…”

Processing of the rne Transcript by an RNase E-independent Amino Acid-dependent Mechanism

“…1. Panel A, two sets of ribonuclease protection assays were analyzed using the internal 32 P-labeled riboprobes corresponding to rne coordinates 2031-1231 (probe a, lanes [1][2][3][4][5] and 2031-1480 (probe b, lanes 6 -10), respectively (The coordinates, T7 promoter, and direction of RNA synthesis are indicated in the schematic drawing.) The RNase protection assay was performed as described under "Materials and Methods" with 10 g of yeast total RNA without ribonuclease digestion (lanes 1 and 6) or with ribonuclease digestion (lanes 2 and 7), with 5 g of in vitro T3 RNA polymerase-synthesized RNA corresponding to 1537-2168 of rne (lanes 3 and 8) or with 2 g of RNA isolated from N3431 at 33°C (lanes 4 and 9) or at 43°C (lanes 5 and 10).…”

“…While RNase E is essential for cell growth, conditional (temperature-sensitive) rne mutants, such as rne-3071 (6, 7) and ams-1 (8,9) have been isolated, and the sites of mutation have been mapped to the N-terminal half of the polypeptide (10), which contains the catalytic domain of the enzyme (11,12). Inactivation of RNase E activity in these temperature-sensitive mutants by culture at nonpermissive temperature prolongs the decay of bulk mRNA and of specific transcripts (4,5).…”

“…RNase E is encoded by the rne (1-3), also known as ams or hmp, gene (for reviews see Refs. 4 and 5) and is a key enzyme in the processing and decay of mRNA, ribosomal RNA, and regulatory RNAs in Escherichia coli (4,5). While RNase E is essential for cell growth, conditional (temperature-sensitive) rne mutants, such as rne-3071 (6, 7) and ams-1 (8,9) have been isolated, and the sites of mutation have been mapped to the N-terminal half of the polypeptide (10), which contains the catalytic domain of the enzyme (11,12).…”