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EcoSal Plus

Domain 4:

Synthesis and Processing of Macromolecules

Exoribonucleases and Endoribonucleases

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  • Authors: Zhongwei Li1, and Murray P. Deutscher2
  • Editor: Susan T. Lovett3
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Biomedical Sciences, Florida Atlantic University, 777 Glades Road, BC308, Boca Raton, FL 33431-0991; 2: Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, P.O. Box 016129, Miami, FL 33101-6129; 3: Brandeis University, Waltham, MA
  • Received 10 June 2004 Accepted 08 September 2004 Published 29 December 2004
  • Address correspondence to Zhongwei Li zli@fau.edu and Murray P. Deutscher mdeutsch@med.miami.edu
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  • Abstract:

    This review provides a description of the known ribonucleases (RNases), focusing on their structures, catalytic properties, genes, physiological roles, and possible regulation. Currently, eight exoribonucleases are known. These are RNases II, R, D, T, PH, BN, polynucleotide phosphorylase (PNPase), and oligoribonuclease (ORNase). Based on sequence analysis and catalytic properties, the eight exoribonucleases have been grouped into four families. These are the RNR family, including RNase II and RNase R; the DEDD family, including RNase D, RNase T, and ORNase; the RBN family, consisting of RNase BN; and the PDX family, including PNPase and RNase PH. Seven well-characterized endoribonucleases are known in . These are RNases I, III, P, E, G, HI, and HII. Homologues to most of these enzymes are also present in . Most of the endoribonucleases cleave RNA in the presence of divalent cations, producing fragments with 3'-hydroxyl and 5'-phosphate termini. RNase H selectively hydrolyzes the RNA strand of RNA?DNA hybrids. Members of the RNase H family are widely distributed among prokaryotic and eukaryotic organisms in three distinct lineages, RNases HI, HII, and HIII. It is likely that contains additional endoribonucleases that have not yet been characterized. First of all, endonucleolytic activities are needed for certain known processes that cannot be attributed to any of the known enzymes. Second, homologues of known endoribonucleases are present in . Third, endonucleolytic activities have been observed in cell extracts that have different properties from known enzymes.

  • Citation: Li Z, Deutscher M. 2004. Exoribonucleases and Endoribonucleases, EcoSal Plus 2004; doi:10.1128/ecosalplus.4.6.3

Key Concept Ranking

Periplasmic Space
0.4610763
Transcription Start Site
0.41711926
Ribosome Binding Site
0.39960718
Basic Amino Acids
0.39340025
Regulatory RNAs
0.35361776
0.4610763

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/content/journal/ecosalplus/10.1128/ecosalplus.4.6.3
2004-12-29
2017-09-25

Abstract:

This review provides a description of the known ribonucleases (RNases), focusing on their structures, catalytic properties, genes, physiological roles, and possible regulation. Currently, eight exoribonucleases are known. These are RNases II, R, D, T, PH, BN, polynucleotide phosphorylase (PNPase), and oligoribonuclease (ORNase). Based on sequence analysis and catalytic properties, the eight exoribonucleases have been grouped into four families. These are the RNR family, including RNase II and RNase R; the DEDD family, including RNase D, RNase T, and ORNase; the RBN family, consisting of RNase BN; and the PDX family, including PNPase and RNase PH. Seven well-characterized endoribonucleases are known in . These are RNases I, III, P, E, G, HI, and HII. Homologues to most of these enzymes are also present in . Most of the endoribonucleases cleave RNA in the presence of divalent cations, producing fragments with 3'-hydroxyl and 5'-phosphate termini. RNase H selectively hydrolyzes the RNA strand of RNA?DNA hybrids. Members of the RNase H family are widely distributed among prokaryotic and eukaryotic organisms in three distinct lineages, RNases HI, HII, and HIII. It is likely that contains additional endoribonucleases that have not yet been characterized. First of all, endonucleolytic activities are needed for certain known processes that cannot be attributed to any of the known enzymes. Second, homologues of known endoribonucleases are present in . Third, endonucleolytic activities have been observed in cell extracts that have different properties from known enzymes.

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Figures

Image of Figure 1
Figure 1

Primary tRNA transcripts may contain one or multiple tRNAs, tRNAs cotranscribed with mRNA or rRNA, or extended flanking sequences ( 23 ). The steps converting a primary transcript to a mature tRNA are indicated by arrows. Initial cleavages by RNase E in the 3′-trailer regions downstream of the tRNA separate tRNAs from associated molecules ( 23 , 24 , 25 ). The resulting long 3′-trailer sequences are then shortened by RNase II and/or PNPase ( 24 ). Once the 3′ end is shortened, maturation of the 5′ end by RNase P can proceed efficiently ( 23 ). Short 3′ trailers may be removed by the action of several exoribonucleases, primarily RNase T or RNase PH, but RNases II, D, and BN can also participate ( 14 ). If the 5′ extra sequence is able to pair with the 3′ end, RNase P may cleave first, resulting in an unpaired 3′ end that is subsequently removed by exonucleolytic trimming ( 21 , 24 ). Otherwise, processing may occur at both ends simultaneously ( 24 ).

Citation: Li Z, Deutscher M. 2004. Exoribonucleases and Endoribonucleases, EcoSal Plus 2004; doi:10.1128/ecosalplus.4.6.3
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Image of Figure 2
Figure 2

The primary transcripts from the seven rRNA operons are among the most complex RNAs made in , and they require multiple RNases to produce the mature RNAs. An important processing step is carried out by RNase III, which cleaves in the double-stranded regions flanking 16S and 23S rRNA ( 63 , 64 , 65 ). The intermediates generated by these cleavages include 17S RNA, which consists of 16S rRNA plus 115 nt at the 5′ end and 33 nt at the 3′ end; pre-23S RNA, which contains an additional 3 or 7 nt at the 5′ end and 7 to 9 nt at the 3′ end; 9S RNA, the precursor to 5S rRNA; and tRNA precursors. RNase E is responsible for the initial processing of 17S and 9S RNA ( 66 , 67 , 68 ). In 17S RNA, the resulting intermediate contains 66 extra residues at the 5′ end which are then efficiently removed by RNase G ( 68 ). The 3′ end of 16S rRNA is thought to be generated by an endonucleolytic activity, as yet unidentified ( 68 , 69 ). The precursor of 5S rRNA, resulting from RNase E cleavage of 9S RNA contains three extra nucleotides at each end ( 66 , 67 ). The extra 3′ residues are removed by RNase T (3′), but the activity that removes the 5′ residues is as yet unknown ( 61 , 70 ). Pre-23S RNA is shortened at its 3′ end by multiple exo-RNases and is completed by RNase T; the activity responsible for removal of the extra residues from the 5′ end is not known ( 62 , Z. Li, S. Pandit, and M. P. Deutscher, unpublished results). All the rRNA transcripts contain one or two tRNAs between 16S and 23S rRNA, and some contain one or two distal tRNAs. The tRNA precursors are matured as described in Fig. 1 .

Citation: Li Z, Deutscher M. 2004. Exoribonucleases and Endoribonucleases, EcoSal Plus 2004; doi:10.1128/ecosalplus.4.6.3
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Figure 3

Double-stranded stems can be formed between the mature 5′ and 3′ ends (in boldface) of many stable RNA species, but not for 16S rRNA ( 21 , 62 ). The presence of such a terminal stem appears to lead to a requirement for exonucleolytic removal of the 3′ extra sequences (in lightface) ( 21 , 24 , 62 ). In contrast, for 16S rRNA, a stable RNA without such a terminal stem, endonucleolytic cleavage appears to be required for maturation of its 3′ end ( 68 , 69 ). These terminal stems may act to limit the 3′-trimming reaction by exoribonucleases, thereby defining the position of the mature 3′ end and stabilizing the mature RNA ( 21 , 71 ).

Citation: Li Z, Deutscher M. 2004. Exoribonucleases and Endoribonucleases, EcoSal Plus 2004; doi:10.1128/ecosalplus.4.6.3
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Tables

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Table 1

exoribonucleases

Citation: Li Z, Deutscher M. 2004. Exoribonucleases and Endoribonucleases, EcoSal Plus 2004; doi:10.1128/ecosalplus.4.6.3
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Table 2

endoribonucleases

Citation: Li Z, Deutscher M. 2004. Exoribonucleases and Endoribonucleases, EcoSal Plus 2004; doi:10.1128/ecosalplus.4.6.3

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