Viruses Know More Than One Way to Don a Cap

COMMENTARY

Viruses know more than one way to don a cap

Eugene V. Koonina,1 and Bernard Mossb,1 aNational Center for Biotechnology Information, National Library of Medicine and bLaboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892

apping of mRNA is an early A Conventional cap formation posttranscriptional event, (i) pppN(pN)n- ppN(pN)n + Pi unique to eukaryotes, that (ii) pppG+ ppN(pN)n- (G5')pppN(pN)n + PPi C fl strongly in uences subsequent (a) E + pppG E-pG + PPi processing, nuclear export, stability, and (b) E-pG + ppN(pN)n- (G5')pppN(pN)n + E translation of mRNA. Accordingly, viruses (iii) G(5')pppN(pN)n + AdoMet m7G(5')pppN(pN)n + AdoHcy of eukaryotes, whether they reside in the (iv) m7G(5')pppN(pN)n + AdoMet m7G(5')pppNm(pN)n + AdhHcy nucleus or cytoplasm, must solve the capping problem for efficient replication. In a Alternative cap formation B (i) pppG ppG + Pi recent issue of PNAS, Ogino et al. (1) (ii) ppG + pppA(pN)n- (G5')pppA(pN)n + PPi demonstrate a distinct mechanism used by (a) E + pppA(pN)n E-pA(pN)n- + PPi vesicular stomatitis virus (VSV), and likely (b) E-pA(pN)n- + ppG (G5')pppA(pN)n + E other nonsegmented negative strand RNA (iii) G(5')pppN(pN)n + AdoMet G(5')pppNm(pN)n + AdoHcy viruses (Mononegavirales), to cap the 5′ (iv) G(5')pppNm(pN)n + AdoMet m7G(5')pppNm(pN)n + AdoHcy end of mRNA. The finding is of interest from biochemical and evolutionary per- Fig. 1. Conventional (A) and alternative VSV (B) mechanisms of mRNA capping. Abbreviations: pppG, spectives and exemplifies the diverse ways GTP; pppN(pN)n-, 5′ end of pre-RNA; E, enzyme; PPi, pyrophosphate; AdoMet, S-adenosylmethionine; that viruses adapt to their hosts. AdoHcy; S-adenosylhomocysteine. A cap, consisting of a 7-methylguanosine (m7G) linked to the 5′ end of the transcript β-sheet core (Fig. S1); however, compar- volved in cap formation that shows sig- by a 5′-5′ triphosphate bridge [m7G(5′) ison of the predicted secondary structure nificant similarity to ribosomal RNA ppp(5′)N- or m7G(5′)ppp(5′)Nm in which of the PRNTase domain to the available Nm is a 2′-O methylated nucleoside], was MTase (13, 14). The identity of the phos- identified in viral and mammalian mRNA protein structures failed to detect any phatase or GTPase that catalyzes the for- structurally similar domains. Thus the viral mation of GDP from GTP (or whether a 35 years ago and was subsequently found fi to be ubiquitous in eukaryotes and their PRNTase domain is so far unique to speci c enzyme is required) in Mono- viruses with a few exceptions among the Mononegavirales, on par with the unique negavirales remains unknown. Crystal latter (2–4). The enzymology of cap bio- capping reaction of these viruses. The structures of L proteins of Mono- histidine residue that in VSV covalently negavirales or their individual domains will genesis, originally deduced for vaccinia vi- ′ rus (5–8), also pertains to eukaryotes (9) binds the 5 -termini of viral mRNAs is be key to understanding their origins (Fig. 1A). In this conventional pathway, conserved in most Mononegavirales but not and evolution. the RNA guanylyltransferase (GTase) in viruses of the genus Novirhabdovirus The various ways that viruses have transfers GMP to the diphosphate end of (Fig. S1). Given the low similarity between coped with the capping problem are pre-mRNA through a covalent enzyme- the homologous domain in Novirhab- described in Table 1. Straightforward ex- GMP intermediate. In contrast, the VSV doviruses to the PRNTase domains of ploitation of the cellular capping machi- polyribonucleotidyltransferase (PRNTase) other Mononegavirales, it remains unclear nery is typical of DNA viruses that activity of the RNA-dependent RNA whether the histidine residue noted by replicate in the nucleus (Table 1). How- polymerase (L) protein transfers the 5′- Ogino et al. (1) in these sequences corre- ever, molecular strategies that make a monophosphorylated pre-mRNA to GDP sponds to the active histidine (Fig. S1) virus independent of the cellular capping through a covalent enzyme-phosphorylated and, consequently, whether Novirhab- enzymes could be a clear advantage. Sev- RNA intermediate (1) (Fig. 1B). The doviruses possess the same capping eral such strategies have evolved in- latter mechanism involves the formation machinery. dependently, including internal initiation of a phosphoamide bond to histidine in- Given the predicted globular structure of translation on uncapped RNAs in pi- stead of lysine, as occurs in the conven- of the PRNTase domain, with a core cornaviruses and their relatives, tional system. There is also a difference β-sheet(s), it seems unlikely that this do- snatching of capped oligonucleotides in the sequence of methylations in the main evolved de novo, from a simple, re- from host premRNAs to initiate viral two systems: guanine-7-methylation pre- petitive structure, as seems to be the case transcription in segmented negative- α cedes 2’-O-methylation in the conven- for many -helical domains in eukaryotes strand RNA viruses, and recruitment of tional system, whereas the order is (12). A more plausible hypothesis is that genes for the conventional, eukaryotic- reversed with VSV (10). a preexisting globular domain was re- type capping enzymes that apparently oc- Extensive sequence database searches cruited by the common ancestor of Mon- curred independently in widely diverse (SI Materials and Methods) confirmed onegavirales but has changed beyond the conservation of the so-called region V recognition (with sequence analysis and of the rhabodvirus L protein (11) fold recognition methods) in the course Author contributions: E.V.K. and B.M. wrote the paper. among all Mononegavirales but failed to of adaptation to the unique capping re- The authors declare no conflict of interest. detect similarity between this region action. The multiple domains of the L See companion article on page 3463. and any available protein sequences proteins of Mononegavirales are generally 1To whom correspondence may be addressed. E-mail: outside Mononegavirales. Secondary highly derived and show little sequence [email protected] or [email protected]. structure prediction indicated that the conservation outside this group of viruses. This article contains supporting information online at www. viral PRNTase is a globular domain with a The exception is the MTase domain in- pnas.org/cgi/content/full/0915061107/DCSupplemental.

www.pnas.org/cgi/doi/10.1073/pnas.0915061107 PNAS Early Edition | 1of2 Downloaded by guest on September 23, 2021 Table 1. The diversity of solutions to the capping problem among the major groups of viruses of eukaryotes Capping apparatus or alternative Groups of viruses

Utilization of host capping apparatus. Not known Single and double-strand DNA viruses that replicate in the nucleus of animals whether some might modify the cellular capping machinery. and plants: e.g., adenoviruses, herpesviruses, papovaviruses, parvoviruses, reverse-transcribing viruses: retro- and pararetroviruses, hepadnaviruses.

No cap, mRNAs with triphosphate 5′-termini, internal Small positive-strand RNA viruses of plants including carmoviruses, initiation of translation, 3′ translational enhancer. tombusviruses, poleroviruses, luteoviruses. Double-stranded RNA viruses of fungi (totiviruses).

No cap, mRNAs covalently linked to a small protein, Small positive strand RNA viruses of the picorna-like superfamily (picornaviruses, internal initiation of translation. caliciviruses, comoviruses, potyviruses). Double-stranded RNA viruses: birnaviruses.

Reutilization of host caps mediated by virus-encoded Segmented negative-strand RNA viruses: orthomyxoviruses, arenaviruses, mRNA-endonuclease. bunyaviruses.

Virus-encoded capping apparatus,apparently host-derived: Positive-strand RNA viruses: alpha-like superfamily, ﬂaviviruses. Double- RNA triphosphatase, GTase, m7G-MTase; 2’-O-MTase. stranded RNA viruses: reoviridae. Large Nucleocytoplasmic DNA Viruses (NCLDV: poxviruses, asfarviruses, some iridoviruses, phycodnaviruses, mimiviruses); baculoviruses, nudiviruses.

Unique virus-encoded capping apparatus: PRNTase, Mononegavirales (four families: rhabdoviruses, bornaviruses, ﬁloviruses and MTase, GTPase(?) paramyxoviruses).

No homologs of PRNTase or MTase domains. Might use Ophioviridae family of negative-strand RNA viruses infecting plants. host capping apparatus or possess unique set of Order not assigned. The closest known relative of Mononegavirales. capping enzymes.

groups of viruses (Table 1). The discovery group of plant negative strand RNA vi- viral genome sequencing from diverse of Ogino et al. (1) adds the unprecedented ruses that is the closest relative of hosts, it will be of major interest to strategy of evolving a unique capping Mononegavirales judging by the RNA pol- see whether the unique capping ma- apparatus in Mononegavirales. The source ymerase sequence, encode no homologs of chinery discovered in Mononegavirales of recruitment seems clear for the the capping domains. How these viruses recurs in any other viruses and whether MTase domain but not for the PRNTase solve the capping problem remains un- other, yet undiscovered, capping systems domain. Interestingly, ophioviruses, the certain. With the current rapid progress of might exist.

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