RNA-dependent RNA polymerase

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RNA-dependent RNA polymerase
RNA-dependent RNA polymerase
Ribbon representation of the RNA-dependent RNA polymerase, according to PDB  3PHU
Identifier
External IDs
Enzyme classification
EC, category 2.7.7.48 ,  transferase
Substrate Nucleoside triphosphate + RNA n
Products Diphosphate + RNA n + 1

RNA-dependent RNA polymerases (English R NA d ependent R NA p Polymerase ; RdRP or RDR ) are enzymes known as polymerases the synthesis of ribonucleic acids (RNA) of ribonucleotides catalyze the basis of an RNA template (RNA-dependent). They are also referred to as RNA replicases , provided that they build up an RNA that is complementary to it using an RNA strand and can in turn use this as a template for replication .

In the case of various RNA viruses , an RdRP is required to increase their genetic information, for example in the case of the poliovirus . In eukaryotic cells (of animals, plants and fungi), however, RdRPs are used in the course of RNA interference to build double-stranded RNA, which is then broken down; thus they can also be useful in warding off infection with RNA viruses.

RNA-dependent RNA polymerases are a group of RNA polymerases , another are DNA-dependent RNA polymerases , as they are required for the transcription of DNA sections. There are also independent RNA polymerases, for example in polyadenylation .

properties

RNA-dependent RNA polymerase (RdRP) is an essential protein in RNA viruses that is encoded in genomes of viruses that contain RNA and not DNA. It catalyzes the synthesis of an RNA strand complementary to another RNA template. Replication of the RNA is a two-step process. The initiation of the RNA synthesis begins at or near the 3 'end by a primer- independent ( de novo ) or primer-dependent mechanism that uses the protein VPg ( viral protein genome-linked ) as a primer. The de novo initiation consists of adding a nucleoside triphosphate to the 3′-OH end of the first initiating NTP . During elongation, the nucleotidyl transfer of NTPs is repeated to generate a complementary strand of RNA. In contrast to viral DNA polymerases , RdRPs have no correction function and a significantly increased mutation rate of the RNA produced. This manifests itself in the formation of defective copies as well as in the generation of quasi-species to avoid an immune response in the course of an immune evasion .

The RdRp of many eukaryotes are involved in RNA interference ; these amplify microRNA and small temporal RNA and use siRNA as a primer to produce double-stranded RNA.

history

Viral RdRPs were discovered in the studies of the mengovirus and poliovirus in the early 1960s when it was observed that the RdRP-containing viruses were unresponsive to actinomycin D , a cytostatic that inhibits cellular DNA-dependent synthesis of RNA. On the basis of this lack of reaction it was assumed that a virus-specific enzyme must be present which synthesizes the RNA using an RNA template and not using a DNA template.

The best known RdRP is that of the poliovirus. The viral genome consists of RNA that enters the cell with the help of receptor-mediated endocytosis . From there, the RNA is immediately able to serve as a template for the complementary RNA synthesis. The complementary strand itself is then able to act as a template for the production of new viral genomes, which are further packaged and released from the cell to infect more host cells. The advantage of this method of replication is that no DNA is formed as an intermediate stage and thus the reaction takes place faster and more efficiently. The disadvantage is that there is no "security DNA copy" that can make the information accessible again in the event of information loss.

Many RdRp are located close to membranes and are therefore difficult to research. The best-known RdRPs are 3Dpol (poliovirus), VSIV L ( Vesicular stomatitis virus ) and NS5B ( hepatitis C virus ).

structure

All RNA-dependent RNA polymerases and many DNA-dependent polymerases have a tertiary structure that resembles the shape of a right hand. The domains of the enzymes are therefore divided into "fingers", "palm" and "thumb". Only the “palm” consists of a four-stranded, anti-parallel β-sheet with two α-helices . In addition, the “palm” includes three well-preserved motifs (A, B and C). Motif A (Dx (4,5) -D) and motif C (GDD) are spatially next to each other; Mg 2+ and / or Mn 2+ can bind as cofactors to the asparagine residues of these motifs . The asparagine residues of motif B participate in the selection of certain ribonucleoside triphosphates with the help of dNTPs and thus determine whether RNA is synthesized instead of DNA.

The positions of the domains and the tertiary structure of the active site of many RdRPs, even those with low overall sequence homology , are conserved. The active center is shaped by several motifs that contain a large number of conserved amino acids. After binding the RNA, the “fingers” and “thumbs” of the RdRP close to form a ring and the active center is on the inside of the ring. All RdRp in (+) - stranded RNA viruses are associated with the ER or cell membrane . RdRP are structurally related to RNA-dependent DNA polymerases ( reverse transcriptases ). Favipiravir is an inhibitor of many RdRp .

Conserved regions of the RdRP

Conserved region Position relative to poliovirus RNA Amino acid sequence function
Finger (G) 113 STSAGYPY Binding of the RNA template
Finger (F) 153 PLVT YV K D E LRSKT K VEQGKS R LIEA Binding of the RNA template and NTP
Finger (I) 107 LEALDL Binding of the RNA template
Finger (II) 184 SVAMRMAFGNLIAAFHK Binding of the RNA template
Palm (A) 229 LFAF D YTGY D AS Binding of the 2'- hydroxy group of the NTP and the first cofactor
Palm (B) 293 TSIF N SMINNLIIRTLLLKT Binding of the RNA template and the nucleobase of the NTP
Palm (C) 323 MIAY G DD VIAS Binding of another cofactor and the primer for some RdRp
Palm (D) 338 VDASLLAQSGKDY G LTMTPAD K SAT Binding of the triphosphate group of the NTP
Palm (E) 363 FETVTWENVT F L K RF F RA Binding of the 3 'end of the resulting RNA strand
Thumb (III) 405 KDPRNTQDHVRSLCLL Binding of the resulting RNA double strand

Classification

RNA-dependent RNA polymerases are divided into four virus families:

The RdRp in viruses with (+) - stranded or double stranded RNA can be divided into three subfamilies:

Individual evidence

  1. ↑ EV Koonin, AE Gorbalenya, KM Chumakov: Tentative identification of RNA-dependent RNA polymerases of dsRNA viruses and Their relationship to positive beach RNA viral polymerases. In: FEBS letters. Volume 252, Numbers 1-2, July 1989, pp. 42-46, PMID 2759231 .
  2. ↑ PM Zanotto, MJ Gibbs, EA Gould, EC Holmes: A reevaluation of the higher taxonomy of viruses based on RNA polymerases. In: Journal of virology. Volume 70, Number 9, September 1996, pp. 6083-6096, PMID 8709232 , PMC 190630 (free full text).
  3. ↑ Z. Jin, V. Leveque, H. Ma, KA Johnson, K. Klumpp: Assembly, purification, and pre-steady-state kinetic analysis of active RNA-dependent RNA polymerase elongation complex. In: The Journal of biological chemistry. Volume 287, number 13, March 2012, pp. 10674-10683, doi : 10.1074 / jbc.M111.325530 , PMID 22303022 , PMC 3323022 (free full text).
  4. ↑ CC Kao, P. Singh, DJ Ecker: De novo initiation of viral RNA-dependent RNA synthesis. In: Virology. Volume 287, Number 2, September 2001, pp. 251-260, doi : 10.1006 / viro.2001.1039 , PMID 11531403 (review).
  5. ↑ a b c d Katsuhiko S. Murakami: Nucleic Acid Polymerases. Springer Science & Business Media, 2013, ISBN 978-3-642-39796-7 , p. 323.
  6. ↑ AV Bordería, K. Rozen-Gagnon, M. Vignuzzi: Fidelity Variants and RNA Quasispecies. In: Current topics in microbiology and immunology. Volume 392, 2016, pp. 303-322, doi : 10.1007 / 82_2015_483 , PMID 26499340 .
  7. ^ LM Iyer, EV Koonin, L. Aravind: Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases. In: BMC structural biology. Volume 3, January 2003, p. 1, PMID 12553882 , PMC 151600 (free full text).
  8. ↑ JL Hansen, AM Long, SC Schultz: Structure of the RNA-dependent RNA polymerase of poliovirus. In: Structure. Volume 5, Number 8, August 1997, pp. 1109-1122, PMID 9309225 .
  9. ↑ DW Gohara, p Crotty, JJ Arnold, JD Yoder, R. Andino, CE Cameron: poliovirus RNA-dependent RNA polymerase (3Dpol): structural, biochemical, and biological analysis of conserved structural motifs A and B. In: The Journal of biological chemistry. Volume 275, Number 33, August 2000, pp. 25523-25532, doi : 10.1074 / jbc.M002671200 , PMID 10827187 .
  10. ↑ EK O'Reilly, CC Kao: Analysis of RNA-dependent RNA polymerase structure and function as guided by known polymerase structures and computer predictions of secondary structure. In: Virology. Volume 252, Number 2, December 1998, pp. 287-303, doi : 10.1006 / viro.1998.9463 , PMID 9878607 (review).
  11. ↑ Chundi L. Mandahar: Multiplication of RNA Plant Viruses. Springer Science & Business Media, 2006, ISBN 978-1-402-04725-1 , p. 126.
  12. ↑ underlined = preserved, bold = preserved in all RdRp
  13. ↑ J. Deval, Z. Jin, Y. C. Chuang, C. C. Kao: Structure (s), function (s), and inhibition of the RNA-dependent RNA polymerase of noroviruses. In: Virus research. Volume 234, April 2017, pp. 21-33, doi : 10.1016 / j.virusres.2016.12.018 , PMID 28041960 .
  14. ↑ C. Ferrer-Orta, D. Ferrero, N. Verdaguer: RNA-Dependent RNA Polymerases of Picornaviruses: From the Structure to Regulatory Mechanisms. In: Viruses. Volume 7, number 8, August 2015, pp. 4438-4460, doi : 10.3390 / v7082829 , PMID 26258787 , PMC 4576190 (free full text).
  15. ↑ J. Sourimant, R. K. Plemper: Organization, Function, and Therapeutic Targeting of the Morbillivirus RNA-Dependent RNA Polymerase Complex. In: Viruses. Volume 8, number 9, September 2016, p., Doi : 10.3390 / v8090251 , PMID 27626440 , PMC 5035965 (free full text).
  16. ^ R. Cox, R. K. Plemper: The paramyxovirus polymerase complex as a target for next-generation anti-paramyxovirus therapeutics. In: Frontiers in microbiology. Volume 6, 2015, p. 459, doi : 10.3389 / fmicb.2015.00459 , PMID 26029193 , PMC 4428208 (free full text).
  17. ↑ A.A. Eltahla, F. Luciani, P.A. White, A.R. Lloyd, R.A. Bull: Inhibitors of the Hepatitis C Virus Polymerase; Mode of Action and Resistance. In: Viruses. Volume 7, number 10, September 2015, pp. 5206-5224, doi : 10.3390 / v7102868 , PMID 26426038 , PMC 4632376 (free full text).
  18. ↑ B. Martin, B. Canard, E. Decroly: Filovirus proteins for antiviral drug discovery: Structure / function bases of the replication cycle. In: Antiviral research. Volume 141, May 2017, pp. 48-61, doi : 10.1016 / j.antiviral.2017.02.004 , PMID 28192094 .
  19. ↑ CC Posthuma, AJ Te Velthuis, EJ Snijder: Nidovirus RNA polymerases: Complex enzymes handling exceptional RNA genomes. In: Virus research. Volume 234, April 2017, pp. 58-73, doi : 10.1016 / j.virusres.2017.01.023 , PMID 28174054 .
  20. ↑ G. Lu, P. Gong: A structural view of the RNA-dependent RNA polymerases from the Flavivirus genus. In: Virus research. Volume 234, April 2017, pp. 34-43, doi : 10.1016 / j.virusres.2017.01.020 , PMID 28131854 .
  21. ↑ CD Gunawardene, LW Donaldson, KA White: Tombus virus polymerase: Structure and function. In: Virus research. Volume 234, April 2017, pp. 74-86, doi : 10.1016 / j.virusres.2017.01.012 , PMID 28111194 .
  22. ↑ S. Alphonse, R. Ghose: Cystoviral RNA-directed RNA polymerases: Regulation of RNA synthesis on multiple time and length scales. In: Virus research. Volume 234, April 2017, pp. 135–152, doi : 10.1016 / j.virusres.2017.01.006 , PMID 28104452 , PMC 5476504 (free full text).