Replicase polyprotein 1ab
| Replicase polyprotein 1ab | ||
|---|---|---|
| other names |
|
|
| Occurrence | ||
| Parent taxon | Nidovirals | |
_CoV_genome_org_%26_expr_strategy_(here_SARS-CoV)_-_(B)_pp1b_pred_dom_org_of_9_nidovir_fams.jpg)
Replicase polyprotein 1ab (also called ORF1ab polyprotein or ORF1ab frameshift protein ) is a polyprotein of mainly nidoviruses , which is involved in the transcription and replication of viral ribonucleic acid . The polyprotein contains proteinases , which are responsible for breaking down the polyprotein.
function
The replicase gene of nidoviruses consists of two slightly overlapping ORF , which are called 1a and 1b. In corona , toro , bafini and roniviruses , a polyprotein called pp1ab with a mass of 760-800 kDa is synthesized by ORF1ab. For the expression of the ORF1b-encoded portion of pp1ab, a ribosomal frameshifting is required, which enables a controlled shift in the reading frame with position -1, which is located immediately upstream of the ORF1a stop codon , in a defined ratio of translation events. In arteriviruses pp1ab is significantly smaller with a mass of 345-420 kDa. A proteolytic processing of pp1ab by coronaviruses results in up to 16 non-structural proteins (nsp 1-16), whereas the processing of replicase polyproteins of arteriviruses produces up to 14 non-structural proteins. It is generally accepted that most of the non-structural proteins of replicases are composed of a large protein complex called the replication-transcription complex. The complex is anchored to intracellular membranes and likely also includes a number of cellular proteins. pp1ab exhibits the enzymatic activities of protease, RNA-dependent RNA polymerase , helicase and endoribonuclease .
The vast majority of proteolytic cleavages in pp1ab are mediated by an ORF1a-encoded chymotrypsin- like protease, which is also referred to as 3C-like protease (3CL pro ) due to its similarities to 3C proteases of picornaviruses . The term main protease (M pro ) is also increasingly used for this enzyme, mainly to indicate its key role in the processing of the replicase protein in nidoviruses. In recent years, a large amount of structural and functional information has been gained about the M pro of corona and arteriviruses, which in the case of coronaviruses have also contributed to the development of selective protease inhibitors that inhibit viral replication and thus the M pro of nidoviruses as Research items related to the development of antiviral drugs can be considered. In arteri, corona and toroviruses, M pro is supported by one to four papain-like (accessory) proteases (also called PL pro ), which process the less well conserved N -proximal region of the replicase polyprotein. The domain of PL pro of nidoviruses could contain zinc finger structures and also has deubiquitinating activities, indicating that these proteases could also have functions other than processing the polyprotein. Bafini and Roniviruses have not yet been studied in detail, and it is still unclear whether these viruses use papain-like proteases to process the N -terminal regions of pp1a / pp1ab.
Replicase polyproteins of "large" nidoviruses with genome sizes of more than 26 kb (e.g. from corona, toro, bafini and roniviruses) also have 3′-5′- exoribonuclease (ExoN-) and ribose-2 ′ - O - methyltransferase (MT) activities that are essential for the synthesis of corona RNA, but are not conserved in the much smaller arteriviruses. The exact biological function of ExoN is not yet known in any nidovirus, but the relationship to cellular exonucleases of the DEDD superfamily suggest that ExoN could play a role in the replication cycle of large nidoviruses and, as with the DEDD homologues , with proofreading, Repair and recombination mechanisms are related.
The uridylate- specific endoribonuclease, also called NendoU, is a genetic marker of nidoviruses that cleaves single and double-stranded RNA chains at their uridylate residues. Double-stranded RNA are cleaved upstream and downstream of uridylate residues at GUU or GU sequences, resulting in fragments with 2'-3'-cyclic phosphate ends. 2'- O -ribose-methylated RNA substrates are cleavage-resistant to NendoU, which indicates a functional connection between NendoU and the ribose-2'- O -methyltransferase, which encodes the polyprotein gene ORF1ab of coronaviruses as nsp15 and nsp16 are.
Two other RNA-processing domains, ADP-ribose-1 ″ phosphatase (ADRP) and 3 ', 5'-cyclonucleotide phosphodiesterase (CPD), are conserved in overlapping families of nidoviruses. With the exception of the arteri and roniviruses, all nidoviruses encode an ADRP domain which is part of a large replicase subunit (nsp3 in the case of the coronaviruses). The ADRP homolog of the coronavirus has ADP-ribose-1 ″ -phosphatase and poly (ADP-ribose) -binding activities. Although the highly specific phosphatase activity is not essential for viral replication in vitro , the strict preservation in all genera of the coronavirus indicates an important (although currently unclear) function of the protein in the viral replication cycle. This could be related to the functions of the host cell and in particular to the activities of cellular homologs, so-called “macro” domains, which are believed to be involved in the metabolism of ADP-ribose and its derivatives.
ORF1a of all nidoviruses encodes a number of (putative) transmembrane proteins , such as the non-structural proteins 3, 4 and 6 of the coronaviruses and the non-structural proteins 2, 3 and 5 of the arteriviruses. These have been shown or postulated to induce modification of cytoplasmic membranes, including the formation of unusual double membrane vesicles (DMV). The combination of the replication-transcription complex with the virus-induced membrane structures could provide the basic structure or a subcellular compartment for the viral RNA synthesis, whereby the synthesis could possibly also take place under complicated conditions.
Finally, recent structural and biochemical studies have provided new insights into the function of small non-structural proteins encoded in the 3'-terminal portion of the coronavirus ORF1a. For example, nsp7 and nsp8 have been shown to form a hexadecameric super-complex capable of orbiting the dsRNA. It was also possible to show that the coronavirus nsp8 has an RNA polymerase activity ( primase ) which can produce primers that are required by the primer-dependent RNA-dependent RNA polymerase (RdRp), which is located in the nsp12 become. For nsp9 and nsp10, RNA binding activities were detected and crystal structures developed. Nsp10 is a zinc binding protein that contains two zinc finger binding domains and is involved in the synthesis of negative strand RNA .
As with the other nidoviruses, the coronavirus replicase is the replication machinery of the coronavirus. It is organized in subunits that work together and support each other in their respective functions. These subunits are called non-structural proteins (NSPe) and are numbered in the form: nsp1, nsp2, nsp3,….
Nsp1 to nsp10 occur in both replicase protein 1a and 1ab, but sometimes with slightly different functions. Nsp11 only belongs to replicase protein 1a. The fact that these proteins are extremely similar is due to the typical polycistronic genome organization of the nidoviruses. In this case, the NSPs nsp1 to nsp10 are formed from the same genome segment in slightly different ways.
The functions of the first two NSPs nsp1 and nsp2 are somewhat unclear. They are highly variable and do not appear to contain any universally conserved areas within the nidoviruses. Along with some of the next few NSPs, they contain a wide range of countermeasures against the host's immune system, particularly the innate immune response . Because of these properties, they support virus replication indirectly instead of being directly involved in it. Some of these statements still apply to the NSPs nsp3 and nsp4.
The NSPs nsp3 to nsp6 contain all functions that are necessary to generate fully functional viral replication organelles. They also contain two proteinases, which are responsible for processing all viral replicase proteins. These two are usually called PL PRO and 3CL PRO , or coronavirus papain-like proteinase ( English coronavirus p apain- l ike pro teinase ) and coronavirus 3C-like proteinase ( English coronavirus 3C-l ike pro teinase ).
The smaller subunits nsp7 to nsp11, which in the case of replicase protein 1a form its end, contain all primer- synthesizing functions and other essential replication aids.
The remaining NSPs nsp12 to nsp16 occur only in the replicase protein 1ab. They contain the other RNA-modifying enzymes that are used for replication, RNA capping and proofreading, see also co- and post-transcriptional and post-translational modification .
Individual evidence
- ↑ a b c d e John Ziebuhr, Eric J. Snijder, Alexander E. Gorbalenya: Virus-encoded proteinases and proteolytic processing in the Nidovirales . Review Article. In: Journal of General Virology . tape 81 , no. 4 . Great Britain April 1, 2000, p. 853–879 , doi : 10.1099 / 0022-1317-81-4-853 , PMID 10725411 (English, full text or PDF full text download website [accessed on May 22, 2020] Please also note the footnote on page 853!).
- ↑ a b L. Enjuanes, AE Gorbalenya, RJ de Groot, JA Cowley, J. Ziebuhr, EJ Snijder: Nidovirales. In: Encyclopedia of Virology . July 30, 2008, pp. 419-430, doi : 10.1016 / B978-012374410-4.00775-5 , PMC 7150171 (free full text).
- ↑ KA Ivanov, T. Hertzig, M. Rozanov, S. Bayer, V. Thiel, AE Gorbalenya, J. Ziebuhr: Major genetic markers of nidoviruses encodes a replicative endoribonuclease. In: Proceedings of the National Academy of Sciences . Volume 101, number 34, August 2004, pp. 12694-12699, doi : 10.1073 / pnas.0403127101 , PMID 15304651 , PMC 514660 (free full text).
- ↑ a b c d e f g Benjamin W. Neuman, Peter Chamberlain, Fern Bowden, Jeremiah Joseph: Atlas of coronavirus replicase structure . In: Virus Research . tape 194 , edition December 16, 2013. Elsevier, December 16, 2013, ISSN 0168-1702 , p. 49–66 , doi : 10.1016 / j.virusres.2013.12.004 , PMID 24355834 , PMC 7114488 (free full text) - (English, full text [PDF; 3.3 MB ; accessed on July 17, 2020]).
- ↑ a b c Ogando NS, Ferron F, Decroly E, Canard B, Posthuma CC and Snijder EJ: The Curious Case of the Nidovirus Exoribonuclease: Its Role in RNA Synthesis and Replication Fidelity . In: Aartjan Te Velthuis (Ed.): Frontiers in Microbiology . tape 10 , article no. 1813, August 7, 2019, doi : 10.3389 / fmicb.2019.01813 , PMID 31440227 , PMC 6693484 (free full text) - (English, full text [PDF; 6.8 MB ; accessed on June 1, 2020]).
- ↑ Khulud Bukhari, Geraldine Mulley, Anastasia A. Gulyaeva, Lanying Zhao, Guocheng Shu, Jianping Jiang, Benjamin W. Neuman: Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae, and from a sister group to the Coronavirinae , the proposed genus Alphaletovirus . In: Virology . tape 524 , November 2018 edition. Elsevier, September 7, 2018, p. 160–171 , doi : 10.1016 / j.virol.2018.08.010 , PMID 30199753 , PMC 7112036 (free full text) - (English, full text [PDF; 3.3 MB ; accessed on May 18, 2020] " Coronavirinae ": today " Orthocoronavirinae ").