Chapter 2 : Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria

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All living organisms, including the Gram-negative bacteria, have two major classes of RNA molecules. mRNAs contain the information for the synthesis of the various proteins that are required for a living cell. The so-called nontranslated RNAs, which include tRNAs, rRNAs, and small regulatory RNAs (sRNAs), provide the RNA components for ribosome assembly, protein synthesis, and the regulation of mRNA functionality based on RNA/RNA interactions. The highly diverse functions that these RNAs perform within the cell are possible due to numerous enzymes that are involved in posttranscriptional RNA metabolism. However, many of these enzymes have overlapping activities. Besides the normal cellular complement of enzymes that carry out the above functions, there are ribonucleases that are specifically associated with particular stress conditions as part of toxin/antitoxin (TA) systems.

Citation: Mohanty B, Kushner S. 2019. Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria, p 19-35. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0011-2017
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Figure 1

Venn diagram of RNases in showing their involvement in the four major RNA metabolic pathways in Gram-negative bacteria. The participation of the various proteins is only included in pathways where it has been established that they play a significant role. In addition, it is possible that some proteins, such as YbeY, are involved in additional pathways.

Citation: Mohanty B, Kushner S. 2019. Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria, p 19-35. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0011-2017
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Figure 2

Model for the initiation of mRNA decay by RNase E. For the sake of simplicity, the other proteins associated with the RNase E-based degradosome are not shown. In addition, this model is independent of whether RNase E is associated with the inner membrane of . 5′ monophosphate RNA, a preferred substrate for RNase E, is degraded via a 5′-end-dependent pathway. In contrast, 5′ triphosphate RNA is degraded via an RNase E internal entry mechanism. Any endonucleolytically cleaved fragments with strong secondary structures, such as one containing a Rho-independent transcription terminator shown here, undergo polyadenylation by PAP I. Subsequently, all decay intermediates are degraded by 3′→5′ exonucleases (PNPase, RNase II, and RNase R) followed by oligoribonuclease to mononucleotides. Figure is not drawn to scale. p, phosphomonoester; ppp, triphosphate.

Citation: Mohanty B, Kushner S. 2019. Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria, p 19-35. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0011-2017
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Figure 3

Diagrammatic representation of four independent pathways of tRNA processing. (A) Processing of the polycistronic operon. RNase E initiates processing by cleaving the polycistronic transcript to release pre-tRNAs ( ). Processing at the 5′ termini is carried out by RNase P. Maturation of the 3′ termini is usually carried out by RNase T and/or RNase PH. If these two enzymes are not present, RNase D and/or RNase BN can complete the process. (B) Processing of the monocistronic transcript ( ). The Rho-independent transcription terminator is removed exonucleolytically by PNPase. In the absence of PNPase, a combination of RNase P and RNase II can digest the terminator. Subsequently, RNase P matures the 5′ terminus, while RNase T and RNase PH complete the process at the 3′ terminus. (C) Processing of the polycistronic operon ( ). RNase P separates and pre-tRNAs by cleaving at their respective mature 5′ ends, while PNPase and RNase II shorten the 3′ Rho-dependent terminator. Subsequently, 3′→5′ exonucleases (RNase T/RNase PH/RNase D/RNase BN) mature the 3′ ends. (D). Processing of the monocistronic transcript ( ). RNase E removes the Rho-independent transcription terminator to generate the mature 3′ terminus without the need of any of the 3′→5′ exonucleases. RNase P cleaves at the mature 5′ end. Figure is not drawn to scale.

Citation: Mohanty B, Kushner S. 2019. Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria, p 19-35. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0011-2017
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Figure 4

Processing of rRNA operons in . The and operons are shown as model operons. RNase III (RIII) cleaves the 30S rRNA transcript first within the double-stranded stems formed by the spacer sequences adjacent to the mature 16S and 23S rRNAs, generating 17S, 25S, and 9S pre-rRNAs. The functional mature 16S rRNA is generated from 17S pre-rRNA after initial RNase E (E) cleavage, followed by RNase G (G) at the mature (M) 5′ end and removal of an extra 33 nucleotides at the 3′ ends by YbeY (Y) along with multiple exoribonucleases (not shown). A p5S precursor is generated from the 9S precursor by initial RNase E cleavage at 3 nucleotides upstream (E) and downstream (E) of the mature termini of the mature 5S rRNA. The mature 5′ ends of the tRNAs are generated by RNase P (P) cleavage. Exoribonucleases (X) (primarily RNase T) are responsible for the 3′ end maturation of the tRNAs, 23S rRNA, and 5S rRNA, but the RNase(s) (?) responsible for the maturation of the 5′ ends of 23S and 5S rRNAs remain unidentified. The model is not drawn to scale.

Citation: Mohanty B, Kushner S. 2019. Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria, p 19-35. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0011-2017
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Table 1

Proteins involved in posttranscriptional RNA metabolism in

Citation: Mohanty B, Kushner S. 2019. Enzymes Involved in Posttranscriptional RNA Metabolism in Gram-Negative Bacteria, p 19-35. In Storz G, Papenfort K (ed), Regulating with RNA in Bacteria and Archaea. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.RWR-0011-2017

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