Messenger
RNAs are decorated by a cap structure, which is essential for their
translation into proteins. Many viruses have developed strategies in
order to cap their mRNAs. The cap is either synthetized by a subset of
viral or cellular enzymes, or stolen from capped cellular mRNAs by viral
endonucleases ('cap-snatching'). Reverse genetic studies provide
evidence that inhibition of viral enzymes belonging to the capping
pathway leads to inhibition of virus replication. The replication defect
results from reduced protein synthesis as well as from detection of
incompletely capped RNAs by cellular innate immunity sensors. Thus, it
is now admitted that capping enzymes are validated antiviral targets, as
their inhibition will support an antiviral response in addition to the
attenuation of viral mRNA translation. In this review, we describe the
different viral enzymes involved in mRNA capping together with relevant
inhibitors, and their biochemical features useful in inhibitor
discovery.
The 5′ end of nascent eukaryotic messenger RNA (mRNA) is co-transcriptionally modified by the addition of a cap structure. The cap-0 structure consists of a guanosine linked by a 5′–5′ triphosphate bridge to the RNA 5′ end (Figure 1a). This cap structure is methylated at the nitrogen in position 7 of G (cap-0 structure or m7GpppN). In metazoan, cap-0 is often converted into cap-1 structure by 2′-O-methylation of the first N1ribose (cap-1 structure or m7GpppN2′m) of the mRNA. This structure plays several key biological functions (reviewed in Ref. [1••]). The cap (i) increases mRNA stability by protecting mRNA from 5′ exoribonucleases; (ii) participates to pre-mRNA splicing and export to the cytoplasm; (iii) ensures the recruitment of mRNA to the ribosomes
by recognizing eukaryotic translation Initiation Factor (eIF4E); and
(iv) initiates the translation of mRNA into proteins. In addition, it
was demonstrated that the cap structure is a marker of ‘self’,
preventing detection by mechanisms of cellular innate immunity [2]. It was first reported that host cell sensors, such as Toll Like Receptor
(TLR) and Retinoic acid-Inducible Gene (RIG)-like receptors, could
detect uncapped RNAs with 5′-triphosphate ends. More recently, it was
also shown that RIG-I and Melanoma Differentiation-Associated protein 5 (MDA5) recognize mis-capped RNA lacking 2′-O-methylation of the first transcribed nucleotide [3, 4] initiating signaling cascades leading to the expression and release of cytokines and type I interferon. In turn, interferon induces an antiviral state in neighboring cells. Among the Interferon-Stimulated Genes (ISG), InterFeron-Induced protein with Tetratricopeptide repeats 1 (IFIT 1) can recognize mis-capped RNAs and inhibit their translation [5].
Figure 1. (a) Chemical structure of the eukaryotic RNA cap. (b) Eukaryotic ‘canonical’ RNA capping pathway, in which the nascent mRNA is sequentially processed by four enzymatic activities,
represented as separate enzymes on the right-side of the reaction (see
text for details). RTPase: RNA 5′-triphosphatase; GTase:
Guanylytransferase; N7 MTase: N7-guanine RNA cap methyltransferase; 2′OMTase: Ribose 2′-ORNA methyltransferase.
Within the host cell, eukaryotic mRNA is generally capped through a ‘canonical’ RNA capping
pathway. It generally requires four sequential reactions, elucidated
four decades ago, catalyzed by an RNA 5′ triphosphatase (RTPase), a
guanylyltransferase (GTase), a guanine N7 methyltransferase (N7-MTase) and a 2′-O-MTase, respectively (Figure 1b).
In contrast, many viruses have evolved their own mRNA capping machinery in order to expedite efficient viral protein
production and escape from innate immunity detection. Remarkably,
pathways of viral mRNA capping are highly diverse but almost converge to
the RNA cap structure common to viral and cellular mRNAs (Figure 1a) [6•]. When viruses express their own set of capping enzymes, four types of RNA capping pathways have been evidenced so far [1••, 6•].
In the first one, viruses use a capping pathway similar to that observed in eukaryotic cells (Figure 1b). The phosphate at the 5′ end of the nascent viral is hydrolyzed by an RTPase activity held by an RTPase or a helicase domain. Concomitantly, a GTP is recruited by a GTPase, often forming a covalent adduct Lys-GMP before the transfer of GMP onto the RNA 5′ diphosphate end [7, 8, 9, 10, 11]. This occurs for DNA viruses (e.g., poxviruses, mimivirus, baculoviruses) as well as supposedly for several positive strand RNA viruses (e.g., flavivirus, coronavirus). After capping, the cap is methylated on its N7 and 2′O position by either one bi-functional N7/2′O-MTases (e.g., flaviviruses [12, 13]), or two separate enzymes (e.g., coronaviruses [14]).
The non-segmented negative strand (NNS) viruses use a distinct RNA capping pathway (Figure 2a). The most studied NNS, VSV, codes for a large (L) protein performing both replication/transcription and capping of viral RNA [15]. The cap synthesis is ensured by a polyribonucleotidyltransferase (PRNTase), which forms a covalent link between a conserved histidine and the nascent viral mRNA. In the presence of GDP, the cap structure is formed and the MTase domain in C terminus of the L protein methylates the cap structure at the ribose 2′O position of the first transcribed nucleotide, followed by the cap-guanine at its N7 position.
Figure 2. (a) Negative Non-Segmented (NNS) virus RNA capping pathway, in which the nascent viral mRNA is sequentially processed by four enzymatic activities,
represented as separate enzymes on the right-side of the reaction.
These enzyme activities are generally present in L,a single large polypeptide chain encompassing the viral RNA-dependent RNA polymerase. The NTPase generates a diffusible GDP molecule, and the spatial arrangement and cross-talk of PRNTase and NTPase is still unclear. (b)Togaviridae (alphavirus-like) RNA virus
capping pathway. The N7-GTP MTase generates a diffusible m7GTP
molecule, and here also, the spatial arrangement and cross-talk of the
N7-GTP MTase and GTase is still unclear. (c)
RNA cap-snatching pathway. Viral RNA-dependent RNA polymerases (RdRp)
have (or may have) an RNA cap-binding site in close proximity to an endonuclease (endoN) and distinct from the polymerase
active site. The size (n) of the snatched capped primer varies within
viral families (see text for details). Abbreviations as in Figure 1, plus the following: PRNTase: GDP Polyribonucleotidyl Transferase; NTPase: nucleoside 5′-triphosphatephosphatase; EndoN: endonuclease.
Togaviridae also synthesize a cap structure using a non-conventional mechanism (Figure 2b). This virus family (and also bamboo mosaic virus, a plant pathogen from the related potexvirus genus) codes for an enzyme (alphavirus nsp1) that methylates the N7 of GTP and forms a covalent His-N7GMP complex [16, 17, 18•].
The methylated GMP is then transferred onto the nascent viral RNA
yielding a cap-0 structure. These viruses do not methylate the 2′O
position of the first transcribed nucleotide, raising the question of
how they escape interferon induction when infecting a mammalian host
cell. The answer may lie in a 5′ hairpin structure at the 5′-end of the
viral mRNA which prevents detection by RIG-like sensors.
Last of the four pathways, viruses from the Arenaviridae, Bunyaviridae and Orthomyxoviridae families use a ‘cap snatching’ strategy: they steal the cap structure from cellular mRNA (Figure 2c). For this purpose, a cap-binding domain of the polymerase (or N protein) first recognizes the 5′ methylated cap-1 of host mRNAs. In Orthomyxoviridae and Bunyaviridae, the cellular mRNA is cleaved 10–20 nucleotides downstream from the cap structure by a viral endonuclease [19, 20••, 21, 22••]. The snatched RNA is shorter (4–7 nucleotides) for the Arenaviridae endonuclease [23].
These short-capped RNAs are subsequently used as primers for viral mRNA
synthesis by the viral polymerase. By using this strategy, viruses kill
two birds with one stone: de-capping of cellular mRNA blocks the
expression of cellular RNA while favoring the expression of viral RNAs.
Enzymes involved in viral RNA capping pathways
5′-RNA triphosphatase
When nascent viral RNA emerges from the viral replicase/transcriptase, the 5′-pppRNA is processed to 5′-ppRNA before being decorated with the guanine cap. There are five types of viral 5′-RNA triphosphatases involved in this first step of the canonical viral RNA capping pathway.
Metazoan metal-independent RTPases, such as that of the baculovirus BVP, constitute the first type [24].
These enzymes belong to the cysteinyl-phosphatase family, whose fold
and catalytic mechanism have a large number of cellular counterparts,
thus limiting its interest as a drug design target for the sake of
selectivity.
In the second type, hydrolysis of
the RNA 5′-γ-phosphate is achieved by genuine metal-dependent dedicated
viral 5′-TPase. This is the case in plant, fungi, protozoans, and DNA viruses (mimivirus, poxviruses, baculoviruses have 2 distinct TPases), with the so-called Triphosphate Tunnel Metallo-enzymes (TTM) superfamily [11, 25].
The metal-dependent active-site lies at the bottom of a tunnel, the
shape of which seems well-suited to accommodate specific inhibitors
exhibiting binding affinities in the nanomolar range [26•]. The third and fourth type are those of Reoviridae, which also have their genuine 5′-RTPase: the HIT-like family of Rotavirus, an octamer of the NSP2, and the so-called RNA cap assembly line, a large enzyme complex encompassing VP4 and λ2 of Bluetongue and mammalian orthoreovirus, respectively [27, 28].
The RNA cap assembly line represents a model of concealing nascent
viral RNA and compaction of a chemical reaction sequence. In the last,
fifth type, hydrolysis of the RNA 5′-γ-phosphate is achieved by the
‘engine’ of the viral helicasewhose NTPase active site is also able to accommodate the 5′-pppRNA [29].
This NTPase active site incorporates a DEAD/H sequence (Walker B motif)
and is responsible for fueling the helicase movement along RNA. An
inhibitor at this site should therefore be bi-functional, killing both
helicase and RTPase/capping activities. However, probably due to the
highly dynamic nature of the helicase enzyme, few potent inhibitors have
been reported so far [30].
Guanylyltransferase
In
the viral RNA capping pathway, GTases are amongst the first enzymes to
have been identified nearly forty years ago, as they form an easily
detectable GMP-enzyme adduct [7, 8, 9, 10, 11]. Biochemical and structural characterization has revealed that GTases belong to the ATP-dependent DNA ligase family [31]. However, only few virus families (some dsDNA viruses and Reoviridae) rely on these ‘pure’ GTases included into the capping pathway between RTPases and RNA cap-MTases. GMP is loaded onto the ε-NH2
of a catalytic lysine part of a KXDG(I/L) motif to form the typical
covalent adduct, which is later transferred to the viral 5′-diphosphate
RNA. A detailed mechanism has been inferred from elegant
crystallographic and mechanistic studies [11]. Few GTase inhibitors have been isolated yet (Figure 3).
Mechanistic data might serve to guide the design of active-site
inhibitors, provided that selectivity is achievable amongst the large
number of cellular GMP-transfer enzymes.
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