Escherichia coli cafA Gene Encodes a Novel RNase, Designated as RNase G, Involved in Processing of the 5′ End of 16S rRNA

Wachi, Masaaki; Umitsuki, Genryou; Shimizu, Miwa; Takada, Ayako; Nagai, Kazuo

doi:10.1006/bbrc.1999.0806

Cited by 136 publications

(156 citation statements)

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“…Then, the 33 extra 3Ј-nucleotides are removed by any one of four exoribonucleases, RNase II, R, PH, or PNPase. Removal of the extra 3Ј-residues results in the extra 5Ј-residues becoming single-stranded, which enables the single-strand-specific endoribonuclease, RNase E, to cleave at residue ϩ66 to generate the 16.3S rRNA precursor (5,6). Cleavage at ϩ66 facilitates the subsequent cleavage by RNase G at the mature 5Ј terminus.…”

Section: Discussionmentioning

confidence: 99%

“…In the case of 16S rRNA, the extra 115 nt 2 at the 5Ј end of the molecule are removed in a two-step process that involves cleavage by the endoribonuclease RNase E, at a position 66 nt upstream of the 5Ј end, followed by the action of a second endoribonuclease RNase G, which cleaves at the mature 5Ј terminus (5,6). Thus, 5Ј processing of 16S rRNA involves an ordered sequence of events, and the RNases involved have been identified.…”

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confidence: 99%

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Multiple Exoribonucleases Catalyze Maturation of the 3′ Terminus of 16S Ribosomal RNA (rRNA)

Sulthana

Deutscher

2013

Journal of Biological Chemistry

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Multiple Exoribonucleases Catalyze Maturation of the 3′ Terminus of 16S Ribosomal RNA (rRNA)

Sulthana

Deutscher

2013

Journal of Biological Chemistry

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“…coli RNase E is one of the largest members of a highly conserved RNase family 15 . A catalytic core is contained within the aminoterminal half [16][17][18] of RNase E, which in length and sequence closely resembles its paralogue, RNase G 9,19 (Fig. 1a and Supplementary Fig.…”

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Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover

Callaghan

Marcaida

Stead

et al. 2005

Nature

257

427

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“…We further showed that the catalytic domain binds to nucleotide sequences that define a cleavage site, even when the site is made insensitive to cleavage by 2Ј-O-methyl nucleotide substitutions, and that it stalls at the protected locus, preventing attack on nonmodified target sequences 5Ј to that locus. In contrast to the RNase E catalytic domain, RNase G [also known as CafA protein, MreA protein, Rng (28)(29)(30)(31)], which has extensive sequence homology and size similar to N-Rne (32), broadly similar cleavage specificity (31,33,34), a similar preference for 5Ј-monophosphate termini (31,34), and the ability to complement Rne gene deletions (35), showed no directionality of cleavage of the same substrates.…”

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The catalytic domain of RNase E shows inherent 3′ to 5′ directionality in cleavage site selection

Yin

Vickers

Cohen

2002

Proc. Natl. Acad. Sci. U.S.A.

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RNase E, a multifunctional endoribonuclease of Escherichia coli, attacks substrates at highly specific sites. By using synthetic oligoribonucleotides containing repeats of identical target sequences protected from cleavage by 2 -O-methylated nucleotide substitutions at specific positions, we investigated how RNase E identifies its cleavage sites. We found that the RNase E catalytic domain (i.e., N-Rne) binds selectively to 5 -monophosphate RNA termini but has an inherent mode of cleavage in the 3 to 5 direction. Target sequences made uncleavable by the introduction of 2 -O-methylmodified nucleotides bind to RNase E and impede cleavages at normally susceptible sites located 5 to, but not 3 to, the protected target. Our results indicate that RNase E can identify cleavage sites by a 3 to 5 ''scanning'' mechanism and imply that anchoring of the enzyme to the 5 -monophosphorylated end of these substrates orients the enzyme for directional cleavages that occur in a processive or quasiprocessive mode. In contrast, we find that RNase G, which has extensive structural homology with and size similarity to N-Rne, and can functionally complement RNase E gene deletions when overexpressed, has a nondirectional and distributive mode of action.has a demonstrated role in the processing of ribosomal RNA (1, 2), the chemical degradation of bulk cellular RNA (3-7), the decay of specific regulatory, messenger, and structural RNAs (for recent reviews, see refs. 8 and 9), the control of plasmid DNA replication (10), and the removal of poly(A) tails from transcripts (11,12). RNase E cleaves preferentially at specific sites in single-strand RNA segments rich in AϩU nucleotides (13)(14)(15)(16)). An inherent mode of action involving entry of RNase E at the 5Ј end of substrates followed by a 5Ј to 3Ј wave of cleavages has been inferred from the greater in vivo stability of fragments at the 3Ј ends of certain RNA substrates (17-20) together with evidence that (i) the enzyme prefers a free 5Ј end for endonucleolytic cleavage (18,20), (ii) RNase E degradation efficiency is affected by 5Ј-phosphorylation in vivo (10) and in vitro (19,20), and (iii) 5Ј regions of secondary structure can impede cleavages in vivo (21). However, RNA degradation in vivo also can occur in the opposite direction (e.g., ref. 22).As RNase E cleavage of complex substrates potentially can be affected by differences in the affinity of the enzyme for target sites having different sequences (15, 16), by secondary structure (23), and in vivo also by the attachment of ribosomes (24-26) and͞or RNA-binding proteins (27), conclusions about the inherent mode of action of RNase E from studies of long natural substrates may be problematical. We wished to elucidate the mechanism of target-site selection by RNase E in the absence of these confounding factors; to do this, we designed, and chemically synthesized, oligoribonucleotide substrates that contain repeats of identical target sequences and are devoid of regions able to engage in base paring. We found that the RNase E catalytic...

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Escherichia coli cafA Gene Encodes a Novel RNase, Designated as RNase G, Involved in Processing of the 5′ End of 16S rRNA

Cited by 136 publications

References 28 publications

Multiple Exoribonucleases Catalyze Maturation of the 3′ Terminus of 16S Ribosomal RNA (rRNA)

Multiple Exoribonucleases Catalyze Maturation of the 3′ Terminus of 16S Ribosomal RNA (rRNA)

Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover

The catalytic domain of RNase E shows inherent 3′ to 5′ directionality in cleavage site selection

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