Ribonuclease E

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Ribonuclease E
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EC no. 3.1.26.12
CAS no. 76106-82-6
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Ribonuclease E is a bacterial ribonuclease that participates in the processing of ribosomal RNA (9S to 5S rRNA) and the chemical degradation of bulk cellular RNA.

Contents

Cellular localization

RNase E was suggested to be a part of the cell membrane protein complex, as it sediments with ribosomes and crude membranes. Microscopy has localized tagged RNase E to the inner cytoplasmic membrane or a helical cytoskeletal structure closely associated with the inner layer.

Protein structure

This enzyme contains 1,061 residues and separates into two distinct functional regions, which are a large domain located at the 5'N-terminus and a small domain located at the 3' C-terminus. [1] While N-terminal half forms a catalytic domain, C-terminal half forms a degradosome [2] scaffolding domain. A metal-binding pocket separates them in the middle of the RNase E protein structure. [3] Although degradosome formation does not play a key role for E. coli growth, [4] [5] [6] the deletion of the C-terminal half has been found to decrease the rate of decay of some RNase E substrates. [7] [8]

Ribonuclease E function in tetrameric conformation, which contains four subunits associate with each other to create a structure that looks like two scissors connected at the handle region. The scissor blade is made of a large domain, and the handle is made of the small domain. In the catalytic site of the large domain, there are four subdomains that include an RNase H subdomain, a DNase I subdomain, an S1 subdomain, and a 5' sensing region. These four subunits are divided base on their function and similarity to homologous structural folds. RNase H is located at the beginning of N-terminal and named after the RNase H endoribonuclease family since they share a similar structure; however, RNase H serves as a structural function rather than catalytic function because it is lack of active-site residue. [9] [10] Next, the S1 subdomain and 5' sensing region are implanted in RNase H fold. The RNase E S1 domain adopts an OB-fold in which flexible loops are attached to a well-ordered five-stranded β-barrel core. [11] In the ribonuclease E, the S1 domain not only aids in the formation of the tetrameric quaternary structure by dimerization but also serves as a substrate-binding site to facilitate RNA hydrolysis by the catalytic domains within this tetrameric enzyme. [12] [11] With S1 subdomain, 5' sensing region functions as a substrate-binding site that helps to stabilize the target RNA molecule on one subunit so that the other subunit within a dimer can cleave the RNA of interest. [11] The 5' sensing region located at a distance from the catalytic site, which resides on the DNase I subdomain. The last subdomain of the RNase E catalytic site is DNase I, which is named for its conformational similarity to an endonuclease structure that cleaves double-stranded DNA. [9] In ribonuclease E, DNase I subdomain self-complements to dominate the dimer interface. [10] [11] Also, there is two magnesium ion binding site that mediates cleavage by hydrolytic attack of the RNA backbone and two zinc ion binding site that aids in stabilization of a dimer made of two subunits. [3]

Function

Escherichia coli endoribonuclease E has a significant influence on gene expression. It is not only essential for the maturation of ribosomal RNA (rRNA) and transfer RNA (tRNA) but also the rapid degradation of messenger RNA [13] (mRNA) by hydrolysis reaction.

In the maturation of rRNA precursor, the substrates for processing are not naked RNAs but somewhat incomplete, unmodified pre-rRNA-ribosomal protein complexes. Both pre-16S and pre-23S rRNAs are excised from the primary RNA-protein complex by RNase III, which activates subsequent steps in rRNA maturation by generating 5' monophosphorylated cleavage products. RNase E further shortens the 17S precursor of 16S rRNA. This action helps to facilitate 5' maturation of rRNA by RNase G [14] and make two cleavages to excise pre-5S rRNA. In the case of tRNAs, approximately 50 of the 86 tRNA species in E. coli require RNase E. The ribonuclease E cleaves tRNA-containing primary transcripts in the 3' end of the tRNAs. These cleavages serve to separate individual tRNA precursors and to separate tRNAs from mRNAs or terminator sequences. The primary function of ribonuclease E is to cleave at a site beyond the mature 3' end to enable access by 3' exonucleases. [15] [16]

In mRNA degradation, ribonuclease E recognizes and cleaves the single-stranded RNA in A- and U-rich regions. [9] The RNase E catalytic domain binds selectively to 5′-monophosphate RNA termini but has a mode of cleavage in the 3′ to 5′ direction. RNase E can identify cleavage sites by a 3′ to 5′ scanning mechanism. [17] The anchor of the RNase E to the 5′-monophosphorylated end of these substrates orients the enzyme for directional cleavages that occur in a processive mode. In the absence of RNA, the S1 subdomain and 5′ sensing site of RNase E are both exposed to the surrounding solvent, allowing RNA to bind readily. In the presence of RNA, target RNA binds to the combined S1 subdomain and 5′ sensor in the open configuration. The RNA is anchored primarily by the binding affinity of the 5′ sensor and oriented by the hydrophobic surface patch on the S1 subdomain. While the S1 subdomain is acting to orient the molecule, the 5′ sensing pocket likely contributes a significant portion of the substrate-binding affinity. These two sites hold the RNA while the fusion 5/S1 subdomain moves as a single complex into the closed configuration. It brings the substrate into proximity to the catalytic site where a hydroxyl group attacks the phosphate backbone by nucleophilic attack reaction. This response is mediated by magnesium ion. When the RNA of interest is cleaved, and the products of the reaction are eventually released as RNase E returns to the open configuration. Besides, RNase E can be self-regulated whereby the mRNA of ribonuclease E serves as a sensor for total cellular RNase E activity and thus limits RNase E activity due to the availability of substrates and changes of growth rate. [2]

Comparison ribonuclease E of E. coli and other organisms

Based on the alignment for sequences of different bacteria correlated to ribonuclease E of Escherichia coli , it appears that about 70% of the sequences are highly conserved at the beginning of sequences and poorly conserved toward the end of sequences. When comparing the five other organisms' sequences to the sequence of the ribonuclease E, it looks like most of the sequences share the same residues at the N-terminal since the member from ribonuclease E/G family has the same hydrolyze function. [10] In other words, the large catalytic domain of the ribonuclease E/G family member is almost the same. In contrast, the small structural domain, which is located at the C-terminus, is varied for different organisms since the small domain contains a structural sequence that serves as scaffolding for other enzymes. [3] [10] For instance, the ribonuclease E that is in the Cedecea davisae came from the S3JYP0 gene. [18] When observing the structure of the ribonuclease E in Cedecea davisae, the catalytic domain contains S1 motif positioned at 31-119 residue on the sequence and a metal-binding site placed at the 404-407 residue on the sequences which are the same position as S1 domain and metal-binding domain on RNase E of Escherichia coli . [18]

Evolutionary history

Ribonucleases (RNases) protein family involved mainly in RNA metabolism, playing essential roles in RNA maturation, RNA end-turnover, and the degradation of aberrant RNAs or expired species in the cell. [19] They are classified into exoribonucleases and endoribonucleases based on their degradative activities. Ribonuclease E (RNase E) was initially discovered as an endoribonuclease from Escherichia coli strain K12. Based on DNA sequence analysis, orthologs of E. coli RNase E were predicted to exist among dozens of evolutionarily different bacterial species. In E. coli, the ribonuclease E enzyme plays an essential part in controlling cell viability by regulating RNA metabolism, such as the decay of most mRNAs and activates the processing of pre-tRNAs. [20] Besides the degradative function, RNase E is necessary for the maturation of precursors of 5S ribosomal RNA, tRNAs, and the M1 RNA component of the RNase P ribozyme. [20] [3]

Related Research Articles

<span class="mw-page-title-main">Ribonuclease</span> Class of enzyme that catalyzes the degradation of RNA

Ribonuclease is a type of nuclease that catalyzes the degradation of RNA into smaller components. Ribonucleases can be divided into endoribonucleases and exoribonucleases, and comprise several sub-classes within the EC 2.7 and 3.1 classes of enzymes.

<span class="mw-page-title-main">Ribonuclease H</span> Enzyme family

Ribonuclease H is a family of non-sequence-specific endonuclease enzymes that catalyze the cleavage of RNA in an RNA/DNA substrate via a hydrolytic mechanism. Members of the RNase H family can be found in nearly all organisms, from bacteria to archaea to eukaryotes.

<span class="mw-page-title-main">Dicer</span> Enzyme that cleaves double-stranded RNA (dsRNA) into short dsRNA fragments

Dicer, also known as endoribonuclease Dicer or helicase with RNase motif, is an enzyme that in humans is encoded by the DICER1 gene. Being part of the RNase III family, Dicer cleaves double-stranded RNA (dsRNA) and pre-microRNA (pre-miRNA) into short double-stranded RNA fragments called small interfering RNA and microRNA, respectively. These fragments are approximately 20–25 base pairs long with a two-base overhang on the 3′-end. Dicer facilitates the activation of the RNA-induced silencing complex (RISC), which is essential for RNA interference. RISC has a catalytic component Argonaute, which is an endonuclease capable of degrading messenger RNA (mRNA).

In molecular biology, endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some, such as deoxyribonuclease I, cut DNA relatively nonspecifically, while many, typically called restriction endonucleases or restriction enzymes, cleave only at very specific nucleotide sequences. Endonucleases differ from exonucleases, which cleave the ends of recognition sequences instead of the middle (endo) portion. Some enzymes known as "exo-endonucleases", however, are not limited to either nuclease function, displaying qualities that are both endo- and exo-like. Evidence suggests that endonuclease activity experiences a lag compared to exonuclease activity.

<span class="mw-page-title-main">Exonuclease</span> Class of enzymes; type of nuclease

Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain. A hydrolyzing reaction that breaks phosphodiester bonds at either the 3′ or the 5′ end occurs. Its close relative is the endonuclease, which cleaves phosphodiester bonds in the middle (endo) of a polynucleotide chain. Eukaryotes and prokaryotes have three types of exonucleases involved in the normal turnover of mRNA: 5′ to 3′ exonuclease (Xrn1), which is a dependent decapping protein; 3′ to 5′ exonuclease, an independent protein; and poly(A)-specific 3′ to 5′ exonuclease.

<span class="mw-page-title-main">Ranpirnase</span> Enzyme from the Northern Leopard Frog

Ranpirnase is a ribonuclease enzyme found in the oocytes of the Northern Leopard Frog. Ranpirnase is a member of the pancreatic ribonuclease protein superfamily and degrades RNA substrates with a sequence preference for uracil and guanine nucleotides. Along with amphinase, another leopard frog ribonuclease, Ranpirnase has been studied as a potential cancer and antiviral treatment due to its unusual mechanism of cytotoxicity tested against transformed cells and antiviral activity.

<span class="mw-page-title-main">Ribonuclease P</span> Class of enzymes

Ribonuclease P is a type of ribonuclease which cleaves RNA. RNase P is unique from other RNases in that it is a ribozyme – a ribonucleic acid that acts as a catalyst in the same way that a protein-based enzyme would. Its function is to cleave off an extra, or precursor, sequence of RNA on tRNA molecules. Further, RNase P is one of two known multiple turnover ribozymes in nature, the discovery of which earned Sidney Altman and Thomas Cech the Nobel Prize in Chemistry in 1989: in the 1970s, Altman discovered the existence of precursor tRNA with flanking sequences and was the first to characterize RNase P and its activity in processing of the 5' leader sequence of precursor tRNA. Recent findings also reveal that RNase P has a new function. It has been shown that human nuclear RNase P is required for the normal and efficient transcription of various small noncoding RNAs, such as tRNA, 5S rRNA, SRP RNA and U6 snRNA genes, which are transcribed by RNA polymerase III, one of three major nuclear RNA polymerases in human cells.

<span class="mw-page-title-main">Bovine pancreatic ribonuclease</span>

Bovine pancreatic ribonuclease, also often referred to as bovine pancreatic ribonuclease A or simply RNase A, is a pancreatic ribonuclease enzyme that cleaves single-stranded RNA. Bovine pancreatic ribonuclease is one of the classic model systems of protein science. Two Nobel Prizes in Chemistry have been awarded in recognition of work on bovine pancreatic ribonuclease: in 1972, the Prize was awarded to Christian Anfinsen for his work on protein folding and to Stanford Moore and William Stein for their work on the relationship between the protein's structure and its chemical mechanism; in 1984, the Prize was awarded to Robert Bruce Merrifield for development of chemical synthesis of proteins.

<span class="mw-page-title-main">Ribonuclease III</span> Class of enzymes

Ribonuclease III (RNase III or RNase C)(BRENDA 3.1.26.3) is a type of ribonuclease that recognizes dsRNA and cleaves it at specific targeted locations to transform them into mature RNAs. These enzymes are a group of endoribonucleases that are characterized by their ribonuclease domain, which is labelled the RNase III domain. They are ubiquitous compounds in the cell and play a major role in pathways such as RNA precursor synthesis, RNA Silencing, and the pnp autoregulatory mechanism.

<span class="mw-page-title-main">Exosome complex</span> Protein complex that degrades RNA

The exosome complex is a multi-protein intracellular complex capable of degrading various types of RNA molecules. Exosome complexes are found in both eukaryotic cells and archaea, while in bacteria a simpler complex called the degradosome carries out similar functions.

<span class="mw-page-title-main">Pancreatic ribonuclease family</span> Class of enzymes

Pancreatic ribonuclease family is a superfamily of pyrimidine-specific endonucleases found in high quantity in the pancreas of certain mammals and of some reptiles.

Deoxyribonuclease IV (phage-T4-induced) is catalyzes the degradation nucleotides in DsDNA by attacking the 5'-terminal end.

RNase R, or Ribonuclease R, is a 3'-->5' exoribonuclease, which belongs to the RNase II superfamily, a group of enzymes that hydrolyze RNA in the 3' - 5' direction. RNase R has been shown to be involved in selective mRNA degradation, particularly of non stop mRNAs in bacteria. RNase R has homologues in many other organisms.

The degradosome is a multiprotein complex present in most bacteria that is involved in the processing of ribosomal RNA and the degradation of messenger RNA and is regulated by Non-coding RNA. It contains the proteins RNA helicase B, RNase E and Polynucleotide phosphorylase.

<span class="mw-page-title-main">PPP1R8</span> Enzyme found in humans

Nuclear inhibitor of protein phosphatase 1 is an enzyme that in humans is encoded by the PPP1R8 gene.

<span class="mw-page-title-main">OmpT</span> Bacterial protein

OmpT is an aspartyl protease found on the outer membrane of Escherichia coli. OmpT is a subtype of the family of omptin proteases, which are found on some gram-negative species of bacteria.

Ribonuclease T2 is an enzyme. It is a type of endoribonuclease. This enzyme catalyses the following chemical reaction

<span class="mw-page-title-main">Retroviral ribonuclease H</span>

The retroviral ribonuclease H is a catalytic domain of the retroviral reverse transcriptase (RT) enzyme. The RT enzyme is used to generate complementary DNA (cDNA) from the retroviral RNA genome. This process is called reverse transcription. To complete this complex process, the retroviral RT enzymes need to adopt a multifunctional nature. They therefore possess 3 of the following biochemical activities: RNA-dependent DNA polymerase, ribonuclease H, and DNA-dependent DNA polymerase activities. Like all RNase H enzymes, the retroviral RNase H domain cleaves DNA/RNA duplexes and will not degrade DNA or unhybridized RNA.

tRNA-intron lyase is an enzyme. As an endonuclease enzyme, tRNA-intron lyase is responsible for splicing phosphodiester bonds within non-coding ribonucleic acid chains. These non-coding RNA molecules form tRNA molecules after being processed, and this is dependent on tRNA-intron lyase to splice the pretRNA. tRNA processing is an important post-transcriptional modification necessary for tRNA maturation because it locates and removes introns in the pretRNA. This enzyme catalyses the following chemical reaction:

<span class="mw-page-title-main">Ribonuclease T</span> Class of enzymes

Ribonuclease T is a ribonuclease enzyme involved in the maturation of transfer RNA and ribosomal RNA in bacteria, as well as in DNA repair pathways. It is a member of the DnaQ family of exonucleases and non-processively acts on the 3' end of single-stranded nucleic acids. RNase T is capable of cleaving both DNA and RNA, with extreme sequence specificity discriminating against cytosine at the 3' end of the substrate.

References

  1. ↑ Cohen SN, McDowall KJ (March 1997). "RNase E: still a wonderfully mysterious enzyme". Molecular Microbiology. 23 (6): 1099–106. doi: 10.1111/j.1365-2958.1997.tb02593.x . PMID   9106202.
  2. 1 2 Vanzo NF, Li YS, Py B, Blum E, Higgins CF, Raynal LC, et al. (September 1998). "Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome". Genes & Development. 12 (17): 2770–81. doi:10.1101/gad.12.17.2770. PMC   317140 . PMID   9732274.
  3. 1 2 3 4 Koslover DJ, Callaghan AJ, Marcaida MJ, Garman EF, Martick M, Scott WG, Luisi BF (August 2008). "The crystal structure of the Escherichia coli RNase E apoprotein and a mechanism for RNA degradation". Structure. 16 (8): 1238–44. doi:10.1016/j.str.2008.04.017. PMC   2631609 . PMID   18682225.
  4. ↑ McDowall KJ, Cohen SN (January 1996). "The N-terminal domain of the rne gene product has RNase E activity and is non-overlapping with the arginine-rich RNA-binding site". Journal of Molecular Biology. 255 (3): 349–55. doi: 10.1006/jmbi.1996.0027 . PMID   8568879.
  5. ↑ Lopez PJ, Marchand I, Joyce SA, Dreyfus M (July 1999). "The C-terminal half of RNase E, which organizes the Escherichia coli degradosome, participates in mRNA degradation but not rRNA processing in vivo". Molecular Microbiology. 33 (1): 188–99. doi: 10.1046/j.1365-2958.1999.01465.x . PMID   10411735.
  6. ↑ Ow MC, Liu Q, Kushner SR (November 2000). "Analysis of mRNA decay and rRNA processing in Escherichia coli in the absence of RNase E-based degradosome assembly". Molecular Microbiology. 38 (4): 854–66. doi:10.1046/j.1365-2958.2000.02186.x. PMID   11115119. S2CID   45425029.
  7. ↑ Khemici V, Poljak L, Toesca I, Carpousis AJ (May 2005). "Evidence in vivo that the DEAD-box RNA helicase RhlB facilitates the degradation of ribosome-free mRNA by RNase E". Proceedings of the National Academy of Sciences of the United States of America. 102 (19): 6913–8. Bibcode:2005PNAS..102.6913K. doi: 10.1073/pnas.0501129102 . PMC   1100780 . PMID   15867149.
  8. ↑ Morita T, Kawamoto H, Mizota T, Inada T, Aiba H (November 2004). "Enolase in the RNA degradosome plays a crucial role in the rapid decay of glucose transporter mRNA in the response to phosphosugar stress in Escherichia coli". Molecular Microbiology. 54 (4): 1063–75. doi: 10.1111/j.1365-2958.2004.04329.x . PMID   15522087.
  9. 1 2 3 Callaghan AJ, Marcaida MJ, Stead JA, McDowall KJ, Scott WG, Luisi BF (October 2005). "Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover". Nature. 437 (7062): 1187–91. Bibcode:2005Natur.437.1187C. doi:10.1038/nature04084. PMID   16237448. S2CID   4413278.
  10. 1 2 3 4 Kime L, Jourdan SS, McDowall KJ (2008). "Chapter 12 Identifying and Characterizing Substrates of the RNase E/G Family of Enzymes". RNA Turnover in Bacteria, Archaea and Organelles. Methods in Enzymology. Vol. 447. pp. 215–41. doi:10.1016/S0076-6879(08)02212-X. ISBN   978-0-12-374377-0. PMID   19161846.
  11. 1 2 3 4 Schubert M, Edge RE, Lario P, Cook MA, Strynadka NC, Mackie GA, McIntosh LP (July 2004). "Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces". Journal of Molecular Biology. 341 (1): 37–54. doi:10.1016/j.jmb.2004.05.061. PMID   15312761.
  12. ↑ Callaghan AJ, Grossmann JG, Redko YU, Ilag LL, Moncrieffe MC, Symmons MF, et al. (December 2003). "Quaternary structure and catalytic activity of the Escherichia coli ribonuclease E amino-terminal catalytic domain". Biochemistry. 42 (47): 13848–55. doi:10.1021/bi0351099. PMID   14636052.
  13. ↑ Steege DA (August 2000). "Emerging features of mRNA decay in bacteria". RNA. 6 (8): 1079–90. doi:10.1017/S1355838200001023. PMC   1369983 . PMID   10943888.
  14. ↑ Li, Zhongwei; Pandit, Shilpa; Deutscher, Murray P. (1999-05-17). "RNase G (CafA protein) and RNase E are both required for the 5′ maturation of 16S ribosomal RNA". The EMBO Journal. 18 (10): 2878–2885. doi:10.1093/emboj/18.10.2878. ISSN   0261-4189. PMC   1171368 . PMID   10329633.
  15. ↑ Ow, Maria C.; Kushner, Sidney R. (2002-05-01). "Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli". Genes & Development. 16 (9): 1102–1115. doi:10.1101/gad.983502. ISSN   0890-9369. PMC   186257 . PMID   12000793.
  16. ↑ Li, Zhongwei; Deutscher, Murray (2002-02-01). "RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors". RNA. 8 (1): 97–109. doi:10.1017/S1355838202014929. PMC   1370232 . PMID   11871663.
  17. ↑ Feng Y, Vickers TA, Cohen SN (November 2002). "The catalytic domain of RNase E shows inherent 3' to 5' directionality in cleavage site selection". Proceedings of the National Academy of Sciences of the United States of America. 99 (23): 14746–51. Bibcode:2002PNAS...9914746F. doi: 10.1073/pnas.202590899 . PMC   137490 . PMID   12417756.
  18. 1 2 Martinetti Lucchini G, Altwegg M (July 1992). "rRNA gene restriction patterns as taxonomic tools for the genus Aeromonas". International Journal of Systematic Bacteriology. 42 (3): 384–9. doi: 10.1099/00207713-42-3-384 . PMID   1380286.
  19. ↑ Arraiano CM, Andrade JM, Domingues S, Guinote IB, Malecki M, Matos RG, et al. (September 2010). "The critical role of RNA processing and degradation in the control of gene expression". FEMS Microbiology Reviews. 34 (5): 883–923. doi: 10.1111/j.1574-6976.2010.00242.x . PMID   20659169.
  20. 1 2 Mackie, George A. (2013). "RNase E: at the interface of bacterial RNA processing and decay". Nature Reviews. Microbiology. 11 (1): 45–57. doi:10.1038/nrmicro2930. ISSN   1740-1534. PMID   23241849. S2CID   8549476.
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