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Biased (A→I) hypermutation of animal RNA virus genomes
Biased (A-4)
hypermutation
of animal RNA virus genomes
Roberto Cattaneo University
of Ziirich,
Zurich,
Switzerland
RNA genomes evolve largely on the basis of single point mutations introduced by imprecise RNA polymerases, or by recombination. Clusters of certain transitions (biased hypermutations) were detected first in the genomes of persistent viruses, and in the past year have also been found in the genomes of lytic RNA viruses. A cellular RNA-modifying enzyme probably introduces the clustered transitions and thus contributes to the evolution of RNA viruses. Current
Opinion
in Genetics
and
Development
Introduction
Subsequent studies have revealed that clusters of U+C transitions exist in more than half of the matrix genes of MVs f.?om the brains of patients who have died with subacute sclerosing panencephalitis (SSPE) [2], a rare, but always lethal, disease occurring 5-10 years after acute MV infection [3]. Only a minority of the matrix gene inactivation cases could be accounted for by isolated point mutations [4,5]. Less extensive biased hypermutation events were then identified in the genes for the other four major MV proteins [6-8,901, confirming the suggestion that biased hypermutation can occur in the whole MV genome. Moreover, biased hypermutation events have been detected in the genome of a few other negative-strand RNA viruses [ 10,l 1,12”].
Uridine
4:895-900
The mechanism of the introduction of clusters of transitions in viral genomes remains to be established, but indirect evidence implicates a cellular adenosine deaminase specific for double-stranded RNA (dsRNA) [13-161. MV RNA genomes and antigenomes are covered by nucleocapsid protein and do not form duplex RNA structures, but the exceptional aberrant formation of a RNA duplex involving the negative-strand viral genome and an mRNA is postulated [17]. If a dsRNA adenosine deaminase recognized such an aberrant structure, Is would be produced (Fig. 1). If the genomic RNA, instead of being degraded, is replicated, Is will base-pair with Cs (Fig. 1). When this strand is also replicated, the original As will be replaced by Gs.
Biased hypermutation was discovered in 1988 in the RNA genome of a defective measles virus (MV) recovered from the brain of a patient who had succumbed to an MV-induced neurodegenerative disease [l]. This first case of hypermutation to be described is still the most extensive. 132 of the 266 U residues of one gene were mutated to C (the positive-strand antigenome is considered, in the negative-strand genome these mutations are read as A+G substitutions).
Adenosines
1994,
The prevalence of U+C over A+G hypermutation events (as read in the plus, or antigenomic, RNA strand) [2] can be explained according to the dsRNA adenosine deaminase hypothesis. In MV infections, many more plus-strand RNAs (both mRNAs and antigenomes) than minus-strand RNAs (genomes) are synthesized. This gives a higher probability for plus strands to collapse with minus-strand templates than the opposite. This review deals with recent literature demonstrating biased hypermutation in a few RNA viruses, including lytic ones. The effects of cellular enzymes, including the
Inosines
Cytidine
0 1994 Currenl Opinion in Genetics and Development
Fig. 1. Adenosine deamination, as performed by the dsRNA adenosine deaminase. The highlighted adenosine amino group is substituted by an oxygen producing inosine. Left: adenosine, which basepairs with uridine. Right: inosine, which base-pairs with @dine.
Abbreviations HDV-hepatitis
delta
virus;
k&‘-measles
0 Current
virus;
Biology
SSPE-subacute
Ltd ISSN 0959-437X
sclerosing
panencephalitis. 895
896
Genomes
and evolution
dsRNA adenosine deaminase, on the evolution and expression of viral RNA genomes are also discussed.
The spectrum
of biased hypermutation
events
Biased hypermutation events have been detected in the majority of the genomes of SSPE-derived MVs. Why do these events concern almost exclusively the matrix gene [18-21]? It is probably because of the selection for inactivation ‘of matrix protein function in persistent brain infections [3,18,19]. In persistent infections, not only the whole matrix gene, but also the short intracellular domain of the fusion protein, is altered selectively, whereas the fusion protein extracellular domain remains functional [8,22]. Contrary to the case of matrix gene inactivation, the alteration of the gene region encoding the fusion protein intracellular domain is accounted for preferentially by single point mutations or nucleotide deletions. Why this difference? It is probably because of the limited size of the target (< 200 bp). In most cases of biased hypermutation, probably larger regions are modified and are counter-selected because the
fusion protein extracellular domain has to remain fimctional. Recent experiments provide evidence that biased hypermutation events are in fact quite frequent [23**]. Baczko et al. have examined >70 different MV matrix cDNA clones f&m five different regions of an SSPE brain. Sequence analysis of these clones indicates that at least four hypermutation events occurred during virus propagation in this brain [23**] (Fig. 2). Sequence I, found in 10 clones from three brain regions, differs from a postulated precursor virus (the wild-type strain JM) by seven U+C mutations. Sequence II differs from sequence I by 13 U+C changes (only a single clone with sequence II has been characterized). Not less than 58 clones with sequence III, marked by 88 U+C mutations compared to sequence I, were recovered from all five brain regions. Sequences IV and V, detected in only one brain region, are variants of sequence III marked by additional hypermutation events. Interestingly, the mutations in sequence V are 30 A+G conversions, an event that can be explained by the mod-
r-----l A: B: C: D: E:
Right frontal lobe Left frontal lobe Right occipital lobe Left occipital lobe Cerebellum
IV A: B: c: D: E:
Brain
88 U
30A+C
A: B: c: D: E: 0 1994 Current Opmon
Fig. 2. Clonal
in Cenclics and Devclopmcr
expansion of a hypermutated measles virus (MV) in a human brain. Roman numerals indicate different sequences. The number and quality (U-X or A-G) of the mutations distinguishing two sequences is indicated beside the arrows connecting these sequences. The number of clones obtained for each sequence type in each brain region (A-E) corresponds to the length of the black bars (a length scale is shown above the bars of sequence I). Clonal expansion of the MV with sequence Ill is indicated by a shaded circle. Data are from Baczko et a/. [23**] (see text for details).
Biased hypermutation
ification of an antigenomic negative-strand genome.
plus-strand hybridized
to a
Thus, at least four hypermutation events have occurred during the course of a single MV brain infection, with a fifth event accounting for the production of sequence I. The expansion of MV sequence III in all parts of the brain indicates that this hypermutation event is associated with the clonal selection of the corresponding virus. The fact that sequences IV and V are detected in only one part of the brain demonstrates the occurrence of additional hypermutation events in a gene which is clearly no longer under functional constraints. Not only are hypermutations relatively frequent in persistent viruses, but limited hypermutation events can influence the evolution of lytic viruses (Table 1). In the gene for the polymerase-cofactor protein of an MV vaccine strain adapted to grow in suspension cultures, six U-K transitions were detected in a 600 nucleotide region, in the absence of any additional mutation in this 1750 nucleotide gene [7]. More strikingly, in the Chinese MV vaccine strain Shanghai-191, nine U+C mutations were detected in a 260 nucleotide region encoding the variable carboxy-terminal domain of this protein and the 3’ non-translated region [9*]. These observations strengthen the argument that any region of the MV genome can be modified, but only the rare modification events that confer a selective advantage are propagated.
Table
1: Biased
hypermutation
in four negative-strand Type of infection
Virus
Measles
Persistent,
virus
human
and cultured
Vesicular
stomatitis
virus Human
parainffuenza
References
brain
v.9*1
and
slrain
Persistent
(defective
interfering
panicles)
Persistent,
[1,4-6,20,21,23**]
cells
LyGc, laboratory vaccine
RNA viruses’.
cultured
1101
cells
IllI
virus 3 Respiratory
syncytial
Lytic,
*A repon
[57] suggesting
the evolution viruses)
monoclonal escape
virus
that biased
of hantaviruses
is not completely
(another convincing
(12-I
antibody
mulanls
hypermutation family
is involved
of negative-strand
for reasons
not discussed
in RNA here.
In addition to lytic MVs. lytic respiratory syncytial virus mutants also show clusters of U-K transitions. The gene encoding the major envelope protein of a monoclonal antibody escape mutant has been shown to have nine U-K changes over a -300 nucleotide region, and a largely overlapping region of a second mutant was shown
of animal
RNA virus genomes
Cattaneo
to have 10 U+C changes [12”]. Biased hypermutation events have been detected also in vesicular stomatitis virus and human parainfluenza virus 3 persistent infections [lO,ll] (Table 1). Altogether, these observations indicate that biased hypermutation might occur generally in genomes of negative-strand RNA viruses. (The case of the other RNA viruses is discussed below.) The fixation of hypermutation events in lytic viruses, however, is very rare. On the other hand, limited hypermutation events might have been overlooked and considered to be isolated point mutations; it has been noticed that, even after subtraction of all the recognized cases of hypermutation, the number of U+C transitions in MV antigenomes is significantly higher than the number of all other transitions [18].
The cellular enzyme hypermutation
involved
in biased
The dsRNA adenosine deaminase, originally named RNA-unwinding/modifying activity [13,14], was detected first in frog oocytes [24,25], then in many cell types from organisms throughout the animal kingdom [26]. Its its principal biological function, however, remains a matter of speculation [27,28*]. In vitro studies have demonstrated that this enzyme can deaminate As within intermolecular, as well as intramolecular, RNA duplexes [29]. Recently, it has been shown that ‘A+G’ editing of an mRNA encoding a glutamate receptor subunit [30] depends on the intramolecular double-stranded conformation of the editing template [31’]. This observation corroborates the hypothesis that the dsRNA adenosine deaminase is involved in this process. The apparent A+G mutations detected in cDNAs would result from reverse transcription ‘artefacts’ converting Is+Gs. as discussed above for biased hypermutation. Is RNA editing the principal biological function of the dsRNA adenosine deaminase? Probably not. This enzyme is ubiquitous and probably has an housekeeping function, whereas editing is confined to a family of transcripts expressed in the brain (but see [32]). The main function of the dsRNA adenosine deaminase might be in the initial step for the elimination of duplex RNA hybrids by RNases. Duplex RNAs are very stable energetically and their elimination might require the destabilization of base-pairing, a side effect of adenosine deamination (Fig. 1). Support for this ‘RNA targeting for degradation’ hypothesis has come from the detection of clusters of A+G transitions in Xenopus lawis basic fibroblast growth factor transcripts. An overlapping antisense RNA is produced from this gene, in addition to the sense transcript, at certain stages of embryonic development. The stability of the sense transcript decreases strongly when the antisense RNA is present, but in spite of this fact, cDNAs from the overlap region could be cloned. The cDNAs were found to have -50% of the As altered to Gs [33]. As these observations could not be repeated, the proposal that the dsRNA adenosine deaminase is an housekeeping
897
898
Gnomes
.
and evolution
enzyme involved in RNA degradation Ins been considered with some scepticism [27,28’,34*]. The suggestion that the dsRNA adenosine deaminase is an enzyme involved principally in antiviral response [35] has been dismissed [36,37]. . The definitive answer concerning the main function of the dsRNA adenosine deaminase might come soon. Purification of this enzyme from Xenopus Iaeuis oocytes [38], bovine liver [39] and bovine thymus [40] has been followed rapidly by cDNA cloning [41*]; however, characterization of one enzyme might not reveal the whole story. As the random modification characteristic of biased hypermutation is strikingly dif&rent from the specific modification underlying editing. (but see [16]), it has been speculated that a f&nily of enzymes might exist [32], or that adaptor proteins might influence the activity of the dsRNA adenosine deaminase [27]. Indeed, the existence of protein(s) protecting RNA fi-om modification by the dsRNA adenosine deaminase has been demonstrated recently in Xenopus oocytes [34’], and it is possible that diISerent duplex RNA binding proteins might compete for substrate. As different organs probably have other subsets of duplex RNA binding proteins, it might be significant that biased hypermutation and glutamate receptor RNA editing have both been discovered in brain.
Are other cellular enzymes modification (or in editing)
involved in of RNA genomes?
RNA genomes evolve largely on the basis of single point mutations introduced by imprecise RNA polymerases [42], or by recombination [43]. Additionally, evidence discussed here suggests that at least one cellular enzyme can influence the evolution of laboratory and vaccine viral strains. Do other cellular enzymes influence the evolution or expression of ‘street’ RNA viruses? The answer is probably yes. The hepatitis delta virus (HDV) is a subviral pathogen of humans that requires concurrent infection with the hepatitis B virus to be packaged. The HDV genome is a circular RNA molecule of 1.7 kb, possessing significant intramolecular complementarity and forming an unbranched rod structure [44]. A single HDV nucleotide is modified from U+C in 10-40% of the RNA genomes [45]. (A+G modification of the other strand has been excluded.) This modification depends on the presence of a dsRNA structure, but is independent from viral replication [45.46]. As this specific nucleotide change eliminates the stop codon for the small form of the hepatitis delta antigen, the U+C conversion is a form of RNA editing. The fact that a crude nuclear extract of uninfected cells can be used to perform HDV editing in vitro [46] (but see [47]) indicates that the activity operating the U+C conversion is of cellular origin. If such an activity exists, what is its endogenous substrate? We do have a candidate. One case of U+C edit-
ing has been detected recently in a cellular gene [48], but it is not yet known whether this editing phenomenon is dependent on a dsRNA region. Obviously, cellular RNA-editing enzymes [49] could modifjl the informational content of viral genomes. It should be mentioned that RNA editing of viral genes can also be achieved by stuttering RNA polymerases [50]. Another phenomenon which might be attributable to RNA modification (or to the modification of RNA-DNA duplexes) is G+A hypermutation in retroviruses. Clusters of G-A mutations have been detected in the genomes of two different retroviruses [51-531. Interestingly, G+A transitions are observed preferentially within GA dinucleotides (mutated to AA). It is clear that the mechanism of hypermutation in negative-strand RNA viruses is different fi-om the mechanism introducing another type of transition in retroviruses. As was the case for biased hypermutation [l,lO], G+A mutations in retroviruses were explained initially and tentatively by the direct [51] or indirect [52] action of an error-prone viral polymerase. The action of a cellular enzyme is an alternative which should be considered.
Conclusions
and perspectives
Biased hypermutation events have been detected in four negative-strand RNA viruses. It is predicted that accidental formation of a duplex RNA region in the genome of any RNA virus could lead to adenosine deamination and thus to modification. What about hypermutation events in the genomes of positive-strand RNA viruses, dsRNA viruses, or retroviruses? The genomes of dsRNA viruses (e.g. reoviruses) are not supposed to be modified because they are shielded from the cellular environment; dsRNA segments are formed within nascent subviral particles and remain there [54]. The reasons for the apparent lack of modification of the genomes of positive-strand RNA viruses are less obvious. Many positive-strand RNA virus genomes encode polyproteins and have short non-coding regions, an unfavourable pre-requisite for hypermutation. On the other hand, certain non-coding regions (e.g. the 5’ non-coding region in picornaviruses) are GC-rich. Multiple rounds of modification by an adenosine deaminase would result in a G-rich but A-poor region; possibly modification did in fact occur. Anyway, today, only minor biased hypermutation events might be tolerated in positive-strand RNA genomes. As discussed above, minor hypermutation events might be overlooked by being considered to be single mutations. Retroviruses replicate using only one RNA strand (the plus strand) and reverse transcription. In these special RNA viruses, only ‘A+G’ (but not ‘U+C’) clusters of mutations can arise because of the dsRNA adenosine deaminase. These clusters of mutations should mark preferentially RNA regions forming intramolecular duplex RNA structures. Indeed, a striking biased hypermutation event has been disclosed recently in a highly
Biased hypermutation
duplexed region of the long terminal repeat of a mutant Rous-associated virus type 1. In this region, 37 of the 77 As were converted to Gs [55”]. Interestingly, this mutant lost its polyadenylation function and thus caused increased insertional mutagenesis. Remarkably, the mutant emerged during viral spreading in neural tissue (neuroretinal cells). A+1 modification might have a biological role in another retrovirus. A single A in the long terminal repeat of the human immunodeficiency virus can be modified to inosine, an alteration which is believed to influence gene expression [56]. In conclusion, the evolution of RNA virus genomes might indeed be influenced by cellular enzymes. In the future, certain (recombinant) viruses might be used to investigate the function of cellular RNA-modifying enzymes in viva; these viruses will carry a ‘spare’ gene (i.e., an extra gene or a gene whose function is not necessary in certain propagation modes) ready to be modified by cellular activities.
Acknowledgements
characterized mic domain
on
the
manuscript.
Our
work
on
measles
research grants from the Schweizerische
virus
is funded
RNA virus genomes
by alterations of the persistent
Cattaneo
899
in tbe fusion protein cytoplasmeasles virus. virology 1991,
188:910-915. 9.
Rota
.
quences vaccine
JS, Wang
Z-D,
of the strains.
Rota
PA,
Bellini
Comparison of measles
WJ:
H, F, and N coding genes virus Res 1994, 31:317-330.
of sevirus
Three genes of 10 measles virus (MVJ vaccine strains were sequenced completely. Nine clustered U-C transitions were detected in a gene of a Chinese vaccine strain, an observation confirming that hypermutation events can influence the evolution of lytic viruses. PJ, Nichol ST, Horodyski FM, Holland JJ: Vesicular stomatitis virus defective interfering particles can contain extensive genomic sequence rearrangements and base substitutions. Cell 1984, 36:915-924.
10.
O’Hara
11.
Murphy
12. ..
DC, Dimock K, Kang CY: Numerous transitions in human parainfluenxa virus 3 RNA recovered from persistently infected cells. virology 1991, 181:760-763. Rueda
P, Garcfa-Barren0
B, Melero
JA: Loss of conserved
cys-
teine residues in tbe attachment (C) glycoprotein of two human respiratory syncytial virus escape mutants tbat contain multiple A-G substitutions (hypermutations). virology 1994,
198:653-662. A lytic respiratory syncytial virus was neutralized with a monoclonal antibody recognizing a conserved epitope. The two mutants that escaped from this selection are characterized by clustered A+G transitions tU+C in the positive strand). This observation suggests that similar phenomena could take place in patients suffering from respiratory syncytial virus infections. 13.
I thank Martin A Billeter for helpful discussions and continuous support, Pius Spielhofer and Karin Kaelin for their contributions and Hans Weber and Christian Buchholz for helpful comments
of animal
Bass
BL,
lently
H: An unwinding its double-stranded RNA
Weintraub
modifies
activity substrate.
that covaCell 1988,
55:l b89-1098. 14.
by
Nationalfonds.
RW, Smith JE, Cooperman BS, Nishikura K: A doublestranded RNA unwinding activity introduces structural alterations by means of adenosine to inosine conversions in mammalian cells and Xenopus eggs. Proc Nafl Acad Sci USA 1989,
Wagner
86:2647-2651.
References Papers review,
. .. 1.
and recommended
of particular interest, have been higlighted of special interest of outstanding interest
Cattaneo
period
of
virus
1992,
ter Meulen
panencephalitis. Cattaneo V, Bellini
A,
Eschle
MA:
persistent
D,
Baczko
K, ter
Meulen
V,
Mutations infections.
and
A/I
Cuff
Top Microbial
V, Stephenson JR, Kreth Compr Viral 1983, Rebmann S, Billeter
HW: Subacute l&l 05-l 59.
Im-
sclerosing
20.
Wrol
1989,
21.
Cattaneo R, Schmid A, Spielhofer P, Kaelin K, Baczko K, ter Meulen V, Pardowitz J, Flanagan 5, Rima BK, Udem SA, Billeter MA: Mutated and hyperrnutated genes of persistent measles viruses which caused lethal human brain diseases. Wrology 1989, 173:41 S-425. Kaelin
gene
K: RNA editing in the measles provides an additional protein
University Schmid Billeter
of Zurich; A, Spielhofer MA: Subacute
virus [PhD
phosphoprotein Thesis]. Zurich,
1989:41-l). P, Cattaneo
sclerosing
R, Baczko
panencephalitis
K, ter Meulen
is typically
H, Cattaneo
V,
MA: Biased hypercould be due to unwindRNA. Cell 1989, 56331.
R, Billeter
Billeter MA, Cattaneo R: Molecular biology of defective measles viruses persisting in the human central nervous system. In The paramyxoviruses. Edited by Kingsbury DW. New Plenum
Billeter Schmid
Press;
1991:323-345.
MA, Cattaneo R, Spielhofer P, Kaelin K, Huber M, A, Baczko K, ter Meulen V: Generation and prop
Wong TC, Yamanouchi
virus mutations panencephalitis.
Ayata M, Hirano K: Generalized
tation affecting the that causes subacute 63~54645468.
of cell-associated J Cen
in press.
erties of measles subacute sclerosing 7241367-377.
C, Baczko K, ter Meulen MA: Accumulated measles
A: Matrix protein panencephalitis viruses.
I 1995,
Bass BL, Weintraub
York: 19.
sclerosing
selection of adenosines for RNA adenosine deaminase.
Bass BL:
mutation of viral RNA genomes ing/modification of double-stranded
hypermutations
70:2191-2196.
6.
17.
176:63-74.
R, Schmid A, WJ, Rozenblatt
Preferential by double-stranded
AC,
EMBO
Enami M, Sato TA, Sugiura
subacute
Polson
modification
virus mutations in a case of subacute sclerosing panencephalitis: interrupted matrix protein reading frame and transcription alteration. virology 1986, 154:97-l 07. 5.
16.
18.
R, Billeter
in measles
4.
the annual
55:255-265.
muno/
3.
within
SM, Hirano A, Wong TC: Irreversible modification of measles virus RNA in vitro by nuclear RNA-unwinding activity in human neuroblastoma cells. 1 Wrol 1992, 661769-l 773.
Rataul
hypermutation and other genetic changes measles viruses in human brain infections. Cell
in defective 2.
published as:
Cattaneo R, Schmid Billeter MA: Biased 1988,
reading
1s.
Wong
TC,
Ann
associated NY Acad
Yoshikawa
Sci
Y, Tsuruoka
with 1994,
H,
and localized biased hypermumatrix gene of a measles virus strain sclerosing panencephalitis. I Wrol 1989,
M, Ueda 5, Hirano A: Role of biased in evolution of subacute sclerosing panenfrom progenitor acute measles virus. 1 Wool
Ayata
hypermutation cephalitis virus 1991,
A,
typically
65:2191-2199.
22.
Cattaneo
R, Rose JK: Cell fusion by the envelope glycoproteins of persistent measles viruses which caused lethal human brain disease. I Viral 1993, 67:1493-l 502.
23. ..
Baczko K, Lampe J, Lieben V, Pardowitz I, Budka H,
Clonal brain.
expansion virology
UC, Brinckmann U, ter Meulen Cosby SL, lssene S, Rima BK:
of hypermutated 1993,
197:18&195.
measles
virus
in a SSPE
900
Gnomes
and evolution
These autho’rs were in the exceptional position of being able to study five different parts of a brain of a child who died with an NV-induced neurodegenerative disease. Analysis of > 70 matrix cDNA clones revealed that at least four hypermutation events occurred, and that one of the hypermutated viruses had taken over the entire brain by expanding clonally. 24.
Rebagliati
ized . 2s.
MR,
frog
48S99-605.
Bass
BL, Weintraub
RNA
Biol
1990,
activity
48:607413.
44.
Kim
RNA unwinding and modiiing in primary tissues and cell
activity is lines. MO/
Semin
activity:
fact
and
K: Double-stranded RNA adenosine deamimammaliin RNA editing factor. Semin Cell
U, Nishikura
nase as a potential
30.
B, Kohler
M, Sprengel
R, Seeburg
brain controls a determinant of ion flow channels. Ce// 1991, 67~11-19. 31. .
Higuchi M, Single FN, bum PH: RNA editinn
Kohler
M, Sommer
of AMPA structure
PH: RNA
editing in glutamate-gated
8, Sprengel
in
R, See-
370. This paper strengthens the case that ‘A-&’ editing of mRNA encoding glutamate receptor subunits occurs by a mechanism in which the RNA editing substrate has a double-stranded conformation. Thus, this type of editing might indeed be attributable to the dsRNA adenosine deaminase. 32.
33.
Cattaneo R: RNA duplexes 1994, 4:134-l 36.
covalent growth 34.
Saccomanno
.
contains a factor that adenosine to inosine 14:5425-5432.
A factor, injected whether
guide
base conversions.
Curr
Bio/
D, Kinchner MW: An antisense mRNA directs the modiication of the transcript encoding fibrobtast factor in Xenopus oocytes. Cell 1990, 59:687-696.
Kimelman
L, Bass
Lamb 1989,
36.
Weissmann
37.
Morrissey
RNA
C: Sir&-strand LM,
Kirkegaard
modification
activity
with
RNA.
Nafure
Regulation in human cells. K:
RF, Bass BL: Purification
Hough
stranded
RNA
adenosine
a vengeance. 1989,
Nature
337~41 S-41 6.
of double-stranded MO/ Cell Biol 1991,
of the Xenopus faevis doubledeaminase. 1 Biol Chem 1994,
2699933-9939. 39.
Kim U, Garner
TL, Sanford
T, Speicher
K: Purification and characterization adenosine deaminase from bovine Chem 40.
1994,
O’Connell
stranded 41. .
Proc
Nat/
Kim
U,
26913480-l M, Keller
RNA-specific Acad Wang
Sci USA
cloninR of cDNA inase, > candidate Sci
USA
1994,
47.
48.
D, Murray
49.
1994,
recombination in RNA 176:21-32.
Hepatitis replication.
delta virus: Cell 1990,
JL, Bergmann
1992,
Zheng
Fu TB,
of
Lazinski
human
cis and
Top
Warts functions
re-
61:371-373.
Netter
HJ, Bichko
replication 1994,
Sharma
PM,
S: RNA
editing Dev
J: Editing
Taylor
delta
V, Lazinski
cycle
of
virus.
on the geI viral 1992, J: RNA
D, Taylor
human
hepatitis
editvirus.
delta
in press.
Bowman
M,
Madden
in the Wlms’
1994,
Navaratnam T, Giannoni
D,
hepatitis
SL, Rauscher
tumor
FJ, Sukumar
susceptibility
gene,
WT1.
8~720-731.
N, Morrison JR, Bhattacharya F, Teng B-B, Davidson NO,
Pathak
S, Pate1 D, Funahashi Scott J: The p27 cat-
B mRNA 1993,
editing
enzyme
268:20709-20712.
of messenger
RNA
editing.
Annu
VK, Temin HM: Broad spectrum of in vivo forward mutations, hypermutations, and mutational hotspots in a retroviral shuttle vector after a single replication cycle: substitutions, frameshit% and hypermutations. Proc Nat/ Acad Sci USA 1990,
87:601
g-6023.
Vartanian
J-P, Meyerhans
recombination, ficiency virus Li Y, Kappes BH: Molecular
A, Asia
JC, Conway
S: Selection, immunode-
B, Wain-Hobson
and C/A hypermutation type I genomes. / Wrol JA,
of human 1991,
Price
65:1779-l
RW,
Shaw
788.
JM,
Hahn
characterization of human immunodeficiency virus type 1 cloned directly from uncultured human brain tissue: identification of replication-competent and defective viral genomes. ) viral 1991, 65:3973-3985.
5s. ..
Schiff LA, Fields Virology. Edited 199&l 275-l 306. Felder M-P, Laugier M: Functional and
BN: Reoviruses by Fields BN. D, Yatsula
and
their
New
York:
B, Derek%
replication. Raven
P, Calothv
In Press;
G, Marx
biological properties of an avian variant long terminal repeat containing multiple A to C conversions in the U3 sequence. 1 Viral 1994, 6tI4759-4767.
The first demonstration of biased hypermutation in a retroviral genome. Remarkably, this hypermutation event is strictly confined to the U3 region, in which about half of the As are mutated to Gs. It is possible that initially a larger region of a co-replicating retroviral genome was modified, and that the U3 region was transferred successively to the lytic mutant by recombination. 56.
Sharmeen
Tat-dependent tansactivation
RNA 1 Biol
Curr
TL, Cerin JL: Structural requirein hepatitis delta virus: evidence for editing mechanism. Proc Nat/ Acad Sci
51.
53.
viruses.
KF, Brown
editing
Cattaneo R: Different types Rev Cenet 1991, 25:7i-aa.
52.
pop 1992,
89:7149-7153.
H,
Wu T-T,
virus
lmmunol
1992,
50.
JM, Nishikura
of double-stranded nuclear extracts.
3489.
L, Bass B, Sonenberg
N, Weintraub
adenosine-to-inosine modification response RNA. Proc Nat/ Acad
H, Groudine
M:
of wild-type Sci USA
1991,
8a:ao96-8100. 57.
D, Lim B-U, Kang CY: Molecular characterization of the M genomic segment of the Seoul 80-39 virus; nucleotide and amino acid sequence comparisons with other hantaviruses reveal the evolutionary pathway. Virus Res 1991, 19:47-58.
Antic
in press.
T, Zeng
for double-stranded enzyme for RNA in press.
Casey
Genes
W: Purification and properties of doubleadenosine deaminase from calf thymus.
Y, Sanford
for
nomic RNA 66:4693-4697.
54.
11:3719-3725. 38.
46.
cytoplasm of Xenopus oocytes protects double-stranded RNA from modification. MO/ Cell Biol 1994,
C: Unwinding
RA, Dreyfuss 337:19-20.
JM:
quired
ments for RNA a uridine-to-cytidine
BL: The
probably a cytoplasmic dsRNA-binding protein, protects microduplex RNA from deamination. These studies raise the issue of all dsRNA-binding proteins share endogenous substrates.
3s.
Taylor
RNA
JC, Steinhauer D: Curr Top Microbial
alytic subunit of the apolipoprotein is a cytidine deaminase. J Biol Chem
receptor subunit CIuR-B: a determines position and ef-
baskpaired intron ex& ficiency. Cell 1993, 75:1361-l
Genetic
Biochimie
K, Yoo C, Kim U, Murray JM, Estes PA, Cash FE, SA: Substrate specificity of the dsRNA unwinding/modifying enzyme. EM80 1 1991, l&3523-3532.
La Torre
lmmunol
ing in the
Nishikura Liebhaber Sommer
JJ, De
Lai MMC: Microbial
USA
dsRNA unwinding/modifying Dev Biol 1992, 3:42S-433.
. Biol 1993, 4285-293. This and 1271 are excellent reviews of the dsRNA adenosine deaminase by Kazuko Nishikura and Brenda Bass, the two mothers of this enzyme.
29.
4s.
io:ssa6-5590.
BL: The
Bass
fiction. 28. .
regulated
Holland
ulations as quasispecies. 176: l-20. 43.
A developmentally duplexes. Cell 1987,
Wagner RW, Yoo C, Wrabetz L, Kamholz J, Buchhalter J, Hassan NF, Khalili b, Kim SU, Perussia B, McMorris FA, Nishikura
Cell
42.
RNA injections in fertilunwinding activity. Cell
H:
K: Double-stranded detected ubiquitously 27.
DA:
eggs reveal
1987,
that’unwinds 26.
Antisense an RNA duplex
Melton
The dsRNA adenosine deaminase contains three repeats of a dsRNAbinding motif and sequences conserved in the catalytic centre of other deaminases, including a cytidine deaminase involved in apolipoprotein B RNA editing 1491.
K: Molecular RNA adenosine deamediting. Proc Nat/ Acad
Y, Nishikura
R
Cattaneo,
HGnggerberg,
lnstitut f%r Molekularbiologie 8093 Ziirich, Switzerland.
I. Universidt
Ziirich,
hypermutation
of animal RNA virus genomes
Roberto Cattaneo University
of Ziirich,
Zurich,
Switzerland
RNA genomes evolve largely on the basis of single point mutations introduced by imprecise RNA polymerases, or by recombination. Clusters of certain transitions (biased hypermutations) were detected first in the genomes of persistent viruses, and in the past year have also been found in the genomes of lytic RNA viruses. A cellular RNA-modifying enzyme probably introduces the clustered transitions and thus contributes to the evolution of RNA viruses. Current
Opinion
in Genetics
and
Development
Introduction
Subsequent studies have revealed that clusters of U+C transitions exist in more than half of the matrix genes of MVs f.?om the brains of patients who have died with subacute sclerosing panencephalitis (SSPE) [2], a rare, but always lethal, disease occurring 5-10 years after acute MV infection [3]. Only a minority of the matrix gene inactivation cases could be accounted for by isolated point mutations [4,5]. Less extensive biased hypermutation events were then identified in the genes for the other four major MV proteins [6-8,901, confirming the suggestion that biased hypermutation can occur in the whole MV genome. Moreover, biased hypermutation events have been detected in the genome of a few other negative-strand RNA viruses [ 10,l 1,12”].
Uridine
4:895-900
The mechanism of the introduction of clusters of transitions in viral genomes remains to be established, but indirect evidence implicates a cellular adenosine deaminase specific for double-stranded RNA (dsRNA) [13-161. MV RNA genomes and antigenomes are covered by nucleocapsid protein and do not form duplex RNA structures, but the exceptional aberrant formation of a RNA duplex involving the negative-strand viral genome and an mRNA is postulated [17]. If a dsRNA adenosine deaminase recognized such an aberrant structure, Is would be produced (Fig. 1). If the genomic RNA, instead of being degraded, is replicated, Is will base-pair with Cs (Fig. 1). When this strand is also replicated, the original As will be replaced by Gs.
Biased hypermutation was discovered in 1988 in the RNA genome of a defective measles virus (MV) recovered from the brain of a patient who had succumbed to an MV-induced neurodegenerative disease [l]. This first case of hypermutation to be described is still the most extensive. 132 of the 266 U residues of one gene were mutated to C (the positive-strand antigenome is considered, in the negative-strand genome these mutations are read as A+G substitutions).
Adenosines
1994,
The prevalence of U+C over A+G hypermutation events (as read in the plus, or antigenomic, RNA strand) [2] can be explained according to the dsRNA adenosine deaminase hypothesis. In MV infections, many more plus-strand RNAs (both mRNAs and antigenomes) than minus-strand RNAs (genomes) are synthesized. This gives a higher probability for plus strands to collapse with minus-strand templates than the opposite. This review deals with recent literature demonstrating biased hypermutation in a few RNA viruses, including lytic ones. The effects of cellular enzymes, including the
Inosines
Cytidine
0 1994 Currenl Opinion in Genetics and Development
Fig. 1. Adenosine deamination, as performed by the dsRNA adenosine deaminase. The highlighted adenosine amino group is substituted by an oxygen producing inosine. Left: adenosine, which basepairs with uridine. Right: inosine, which base-pairs with @dine.
Abbreviations HDV-hepatitis
delta
virus;
k&‘-measles
0 Current
virus;
Biology
SSPE-subacute
Ltd ISSN 0959-437X
sclerosing
panencephalitis. 895
896
Genomes
and evolution
dsRNA adenosine deaminase, on the evolution and expression of viral RNA genomes are also discussed.
The spectrum
of biased hypermutation
events
Biased hypermutation events have been detected in the majority of the genomes of SSPE-derived MVs. Why do these events concern almost exclusively the matrix gene [18-21]? It is probably because of the selection for inactivation ‘of matrix protein function in persistent brain infections [3,18,19]. In persistent infections, not only the whole matrix gene, but also the short intracellular domain of the fusion protein, is altered selectively, whereas the fusion protein extracellular domain remains functional [8,22]. Contrary to the case of matrix gene inactivation, the alteration of the gene region encoding the fusion protein intracellular domain is accounted for preferentially by single point mutations or nucleotide deletions. Why this difference? It is probably because of the limited size of the target (< 200 bp). In most cases of biased hypermutation, probably larger regions are modified and are counter-selected because the
fusion protein extracellular domain has to remain fimctional. Recent experiments provide evidence that biased hypermutation events are in fact quite frequent [23**]. Baczko et al. have examined >70 different MV matrix cDNA clones f&m five different regions of an SSPE brain. Sequence analysis of these clones indicates that at least four hypermutation events occurred during virus propagation in this brain [23**] (Fig. 2). Sequence I, found in 10 clones from three brain regions, differs from a postulated precursor virus (the wild-type strain JM) by seven U+C mutations. Sequence II differs from sequence I by 13 U+C changes (only a single clone with sequence II has been characterized). Not less than 58 clones with sequence III, marked by 88 U+C mutations compared to sequence I, were recovered from all five brain regions. Sequences IV and V, detected in only one brain region, are variants of sequence III marked by additional hypermutation events. Interestingly, the mutations in sequence V are 30 A+G conversions, an event that can be explained by the mod-
r-----l A: B: C: D: E:
Right frontal lobe Left frontal lobe Right occipital lobe Left occipital lobe Cerebellum
IV A: B: c: D: E:
Brain
88 U
30A+C
A: B: c: D: E: 0 1994 Current Opmon
Fig. 2. Clonal
in Cenclics and Devclopmcr
expansion of a hypermutated measles virus (MV) in a human brain. Roman numerals indicate different sequences. The number and quality (U-X or A-G) of the mutations distinguishing two sequences is indicated beside the arrows connecting these sequences. The number of clones obtained for each sequence type in each brain region (A-E) corresponds to the length of the black bars (a length scale is shown above the bars of sequence I). Clonal expansion of the MV with sequence Ill is indicated by a shaded circle. Data are from Baczko et a/. [23**] (see text for details).
Biased hypermutation
ification of an antigenomic negative-strand genome.
plus-strand hybridized
to a
Thus, at least four hypermutation events have occurred during the course of a single MV brain infection, with a fifth event accounting for the production of sequence I. The expansion of MV sequence III in all parts of the brain indicates that this hypermutation event is associated with the clonal selection of the corresponding virus. The fact that sequences IV and V are detected in only one part of the brain demonstrates the occurrence of additional hypermutation events in a gene which is clearly no longer under functional constraints. Not only are hypermutations relatively frequent in persistent viruses, but limited hypermutation events can influence the evolution of lytic viruses (Table 1). In the gene for the polymerase-cofactor protein of an MV vaccine strain adapted to grow in suspension cultures, six U-K transitions were detected in a 600 nucleotide region, in the absence of any additional mutation in this 1750 nucleotide gene [7]. More strikingly, in the Chinese MV vaccine strain Shanghai-191, nine U+C mutations were detected in a 260 nucleotide region encoding the variable carboxy-terminal domain of this protein and the 3’ non-translated region [9*]. These observations strengthen the argument that any region of the MV genome can be modified, but only the rare modification events that confer a selective advantage are propagated.
Table
1: Biased
hypermutation
in four negative-strand Type of infection
Virus
Measles
Persistent,
virus
human
and cultured
Vesicular
stomatitis
virus Human
parainffuenza
References
brain
v.9*1
and
slrain
Persistent
(defective
interfering
panicles)
Persistent,
[1,4-6,20,21,23**]
cells
LyGc, laboratory vaccine
RNA viruses’.
cultured
1101
cells
IllI
virus 3 Respiratory
syncytial
Lytic,
*A repon
[57] suggesting
the evolution viruses)
monoclonal escape
virus
that biased
of hantaviruses
is not completely
(another convincing
(12-I
antibody
mulanls
hypermutation family
is involved
of negative-strand
for reasons
not discussed
in RNA here.
In addition to lytic MVs. lytic respiratory syncytial virus mutants also show clusters of U-K transitions. The gene encoding the major envelope protein of a monoclonal antibody escape mutant has been shown to have nine U-K changes over a -300 nucleotide region, and a largely overlapping region of a second mutant was shown
of animal
RNA virus genomes
Cattaneo
to have 10 U+C changes [12”]. Biased hypermutation events have been detected also in vesicular stomatitis virus and human parainfluenza virus 3 persistent infections [lO,ll] (Table 1). Altogether, these observations indicate that biased hypermutation might occur generally in genomes of negative-strand RNA viruses. (The case of the other RNA viruses is discussed below.) The fixation of hypermutation events in lytic viruses, however, is very rare. On the other hand, limited hypermutation events might have been overlooked and considered to be isolated point mutations; it has been noticed that, even after subtraction of all the recognized cases of hypermutation, the number of U+C transitions in MV antigenomes is significantly higher than the number of all other transitions [18].
The cellular enzyme hypermutation
involved
in biased
The dsRNA adenosine deaminase, originally named RNA-unwinding/modifying activity [13,14], was detected first in frog oocytes [24,25], then in many cell types from organisms throughout the animal kingdom [26]. Its its principal biological function, however, remains a matter of speculation [27,28*]. In vitro studies have demonstrated that this enzyme can deaminate As within intermolecular, as well as intramolecular, RNA duplexes [29]. Recently, it has been shown that ‘A+G’ editing of an mRNA encoding a glutamate receptor subunit [30] depends on the intramolecular double-stranded conformation of the editing template [31’]. This observation corroborates the hypothesis that the dsRNA adenosine deaminase is involved in this process. The apparent A+G mutations detected in cDNAs would result from reverse transcription ‘artefacts’ converting Is+Gs. as discussed above for biased hypermutation. Is RNA editing the principal biological function of the dsRNA adenosine deaminase? Probably not. This enzyme is ubiquitous and probably has an housekeeping function, whereas editing is confined to a family of transcripts expressed in the brain (but see [32]). The main function of the dsRNA adenosine deaminase might be in the initial step for the elimination of duplex RNA hybrids by RNases. Duplex RNAs are very stable energetically and their elimination might require the destabilization of base-pairing, a side effect of adenosine deamination (Fig. 1). Support for this ‘RNA targeting for degradation’ hypothesis has come from the detection of clusters of A+G transitions in Xenopus lawis basic fibroblast growth factor transcripts. An overlapping antisense RNA is produced from this gene, in addition to the sense transcript, at certain stages of embryonic development. The stability of the sense transcript decreases strongly when the antisense RNA is present, but in spite of this fact, cDNAs from the overlap region could be cloned. The cDNAs were found to have -50% of the As altered to Gs [33]. As these observations could not be repeated, the proposal that the dsRNA adenosine deaminase is an housekeeping
897
898
Gnomes
.
and evolution
enzyme involved in RNA degradation Ins been considered with some scepticism [27,28’,34*]. The suggestion that the dsRNA adenosine deaminase is an enzyme involved principally in antiviral response [35] has been dismissed [36,37]. . The definitive answer concerning the main function of the dsRNA adenosine deaminase might come soon. Purification of this enzyme from Xenopus Iaeuis oocytes [38], bovine liver [39] and bovine thymus [40] has been followed rapidly by cDNA cloning [41*]; however, characterization of one enzyme might not reveal the whole story. As the random modification characteristic of biased hypermutation is strikingly dif&rent from the specific modification underlying editing. (but see [16]), it has been speculated that a f&nily of enzymes might exist [32], or that adaptor proteins might influence the activity of the dsRNA adenosine deaminase [27]. Indeed, the existence of protein(s) protecting RNA fi-om modification by the dsRNA adenosine deaminase has been demonstrated recently in Xenopus oocytes [34’], and it is possible that diISerent duplex RNA binding proteins might compete for substrate. As different organs probably have other subsets of duplex RNA binding proteins, it might be significant that biased hypermutation and glutamate receptor RNA editing have both been discovered in brain.
Are other cellular enzymes modification (or in editing)
involved in of RNA genomes?
RNA genomes evolve largely on the basis of single point mutations introduced by imprecise RNA polymerases [42], or by recombination [43]. Additionally, evidence discussed here suggests that at least one cellular enzyme can influence the evolution of laboratory and vaccine viral strains. Do other cellular enzymes influence the evolution or expression of ‘street’ RNA viruses? The answer is probably yes. The hepatitis delta virus (HDV) is a subviral pathogen of humans that requires concurrent infection with the hepatitis B virus to be packaged. The HDV genome is a circular RNA molecule of 1.7 kb, possessing significant intramolecular complementarity and forming an unbranched rod structure [44]. A single HDV nucleotide is modified from U+C in 10-40% of the RNA genomes [45]. (A+G modification of the other strand has been excluded.) This modification depends on the presence of a dsRNA structure, but is independent from viral replication [45.46]. As this specific nucleotide change eliminates the stop codon for the small form of the hepatitis delta antigen, the U+C conversion is a form of RNA editing. The fact that a crude nuclear extract of uninfected cells can be used to perform HDV editing in vitro [46] (but see [47]) indicates that the activity operating the U+C conversion is of cellular origin. If such an activity exists, what is its endogenous substrate? We do have a candidate. One case of U+C edit-
ing has been detected recently in a cellular gene [48], but it is not yet known whether this editing phenomenon is dependent on a dsRNA region. Obviously, cellular RNA-editing enzymes [49] could modifjl the informational content of viral genomes. It should be mentioned that RNA editing of viral genes can also be achieved by stuttering RNA polymerases [50]. Another phenomenon which might be attributable to RNA modification (or to the modification of RNA-DNA duplexes) is G+A hypermutation in retroviruses. Clusters of G-A mutations have been detected in the genomes of two different retroviruses [51-531. Interestingly, G+A transitions are observed preferentially within GA dinucleotides (mutated to AA). It is clear that the mechanism of hypermutation in negative-strand RNA viruses is different fi-om the mechanism introducing another type of transition in retroviruses. As was the case for biased hypermutation [l,lO], G+A mutations in retroviruses were explained initially and tentatively by the direct [51] or indirect [52] action of an error-prone viral polymerase. The action of a cellular enzyme is an alternative which should be considered.
Conclusions
and perspectives
Biased hypermutation events have been detected in four negative-strand RNA viruses. It is predicted that accidental formation of a duplex RNA region in the genome of any RNA virus could lead to adenosine deamination and thus to modification. What about hypermutation events in the genomes of positive-strand RNA viruses, dsRNA viruses, or retroviruses? The genomes of dsRNA viruses (e.g. reoviruses) are not supposed to be modified because they are shielded from the cellular environment; dsRNA segments are formed within nascent subviral particles and remain there [54]. The reasons for the apparent lack of modification of the genomes of positive-strand RNA viruses are less obvious. Many positive-strand RNA virus genomes encode polyproteins and have short non-coding regions, an unfavourable pre-requisite for hypermutation. On the other hand, certain non-coding regions (e.g. the 5’ non-coding region in picornaviruses) are GC-rich. Multiple rounds of modification by an adenosine deaminase would result in a G-rich but A-poor region; possibly modification did in fact occur. Anyway, today, only minor biased hypermutation events might be tolerated in positive-strand RNA genomes. As discussed above, minor hypermutation events might be overlooked by being considered to be single mutations. Retroviruses replicate using only one RNA strand (the plus strand) and reverse transcription. In these special RNA viruses, only ‘A+G’ (but not ‘U+C’) clusters of mutations can arise because of the dsRNA adenosine deaminase. These clusters of mutations should mark preferentially RNA regions forming intramolecular duplex RNA structures. Indeed, a striking biased hypermutation event has been disclosed recently in a highly
Biased hypermutation
duplexed region of the long terminal repeat of a mutant Rous-associated virus type 1. In this region, 37 of the 77 As were converted to Gs [55”]. Interestingly, this mutant lost its polyadenylation function and thus caused increased insertional mutagenesis. Remarkably, the mutant emerged during viral spreading in neural tissue (neuroretinal cells). A+1 modification might have a biological role in another retrovirus. A single A in the long terminal repeat of the human immunodeficiency virus can be modified to inosine, an alteration which is believed to influence gene expression [56]. In conclusion, the evolution of RNA virus genomes might indeed be influenced by cellular enzymes. In the future, certain (recombinant) viruses might be used to investigate the function of cellular RNA-modifying enzymes in viva; these viruses will carry a ‘spare’ gene (i.e., an extra gene or a gene whose function is not necessary in certain propagation modes) ready to be modified by cellular activities.
Acknowledgements
characterized mic domain
on
the
manuscript.
Our
work
on
measles
research grants from the Schweizerische
virus
is funded
RNA virus genomes
by alterations of the persistent
Cattaneo
899
in tbe fusion protein cytoplasmeasles virus. virology 1991,
188:910-915. 9.
Rota
.
quences vaccine
JS, Wang
Z-D,
of the strains.
Rota
PA,
Bellini
Comparison of measles
WJ:
H, F, and N coding genes virus Res 1994, 31:317-330.
of sevirus
Three genes of 10 measles virus (MVJ vaccine strains were sequenced completely. Nine clustered U-C transitions were detected in a gene of a Chinese vaccine strain, an observation confirming that hypermutation events can influence the evolution of lytic viruses. PJ, Nichol ST, Horodyski FM, Holland JJ: Vesicular stomatitis virus defective interfering particles can contain extensive genomic sequence rearrangements and base substitutions. Cell 1984, 36:915-924.
10.
O’Hara
11.
Murphy
12. ..
DC, Dimock K, Kang CY: Numerous transitions in human parainfluenxa virus 3 RNA recovered from persistently infected cells. virology 1991, 181:760-763. Rueda
P, Garcfa-Barren0
B, Melero
JA: Loss of conserved
cys-
teine residues in tbe attachment (C) glycoprotein of two human respiratory syncytial virus escape mutants tbat contain multiple A-G substitutions (hypermutations). virology 1994,
198:653-662. A lytic respiratory syncytial virus was neutralized with a monoclonal antibody recognizing a conserved epitope. The two mutants that escaped from this selection are characterized by clustered A+G transitions tU+C in the positive strand). This observation suggests that similar phenomena could take place in patients suffering from respiratory syncytial virus infections. 13.
I thank Martin A Billeter for helpful discussions and continuous support, Pius Spielhofer and Karin Kaelin for their contributions and Hans Weber and Christian Buchholz for helpful comments
of animal
Bass
BL,
lently
H: An unwinding its double-stranded RNA
Weintraub
modifies
activity substrate.
that covaCell 1988,
55:l b89-1098. 14.
by
Nationalfonds.
RW, Smith JE, Cooperman BS, Nishikura K: A doublestranded RNA unwinding activity introduces structural alterations by means of adenosine to inosine conversions in mammalian cells and Xenopus eggs. Proc Nafl Acad Sci USA 1989,
Wagner
86:2647-2651.
References Papers review,
. .. 1.
and recommended
of particular interest, have been higlighted of special interest of outstanding interest
Cattaneo
period
of
virus
1992,
ter Meulen
panencephalitis. Cattaneo V, Bellini
A,
Eschle
MA:
persistent
D,
Baczko
K, ter
Meulen
V,
Mutations infections.
and
A/I
Cuff
Top Microbial
V, Stephenson JR, Kreth Compr Viral 1983, Rebmann S, Billeter
HW: Subacute l&l 05-l 59.
Im-
sclerosing
20.
Wrol
1989,
21.
Cattaneo R, Schmid A, Spielhofer P, Kaelin K, Baczko K, ter Meulen V, Pardowitz J, Flanagan 5, Rima BK, Udem SA, Billeter MA: Mutated and hyperrnutated genes of persistent measles viruses which caused lethal human brain diseases. Wrology 1989, 173:41 S-425. Kaelin
gene
K: RNA editing in the measles provides an additional protein
University Schmid Billeter
of Zurich; A, Spielhofer MA: Subacute
virus [PhD
phosphoprotein Thesis]. Zurich,
1989:41-l). P, Cattaneo
sclerosing
R, Baczko
panencephalitis
K, ter Meulen
is typically
H, Cattaneo
V,
MA: Biased hypercould be due to unwindRNA. Cell 1989, 56331.
R, Billeter
Billeter MA, Cattaneo R: Molecular biology of defective measles viruses persisting in the human central nervous system. In The paramyxoviruses. Edited by Kingsbury DW. New Plenum
Billeter Schmid
Press;
1991:323-345.
MA, Cattaneo R, Spielhofer P, Kaelin K, Huber M, A, Baczko K, ter Meulen V: Generation and prop
Wong TC, Yamanouchi
virus mutations panencephalitis.
Ayata M, Hirano K: Generalized
tation affecting the that causes subacute 63~54645468.
of cell-associated J Cen
in press.
erties of measles subacute sclerosing 7241367-377.
C, Baczko K, ter Meulen MA: Accumulated measles
A: Matrix protein panencephalitis viruses.
I 1995,
Bass BL, Weintraub
York: 19.
sclerosing
selection of adenosines for RNA adenosine deaminase.
Bass BL:
mutation of viral RNA genomes ing/modification of double-stranded
hypermutations
70:2191-2196.
6.
17.
176:63-74.
R, Schmid A, WJ, Rozenblatt
Preferential by double-stranded
AC,
EMBO
Enami M, Sato TA, Sugiura
subacute
Polson
modification
virus mutations in a case of subacute sclerosing panencephalitis: interrupted matrix protein reading frame and transcription alteration. virology 1986, 154:97-l 07. 5.
16.
18.
R, Billeter
in measles
4.
the annual
55:255-265.
muno/
3.
within
SM, Hirano A, Wong TC: Irreversible modification of measles virus RNA in vitro by nuclear RNA-unwinding activity in human neuroblastoma cells. 1 Wrol 1992, 661769-l 773.
Rataul
hypermutation and other genetic changes measles viruses in human brain infections. Cell
in defective 2.
published as:
Cattaneo R, Schmid Billeter MA: Biased 1988,
reading
1s.
Wong
TC,
Ann
associated NY Acad
Yoshikawa
Sci
Y, Tsuruoka
with 1994,
H,
and localized biased hypermumatrix gene of a measles virus strain sclerosing panencephalitis. I Wrol 1989,
M, Ueda 5, Hirano A: Role of biased in evolution of subacute sclerosing panenfrom progenitor acute measles virus. 1 Wool
Ayata
hypermutation cephalitis virus 1991,
A,
typically
65:2191-2199.
22.
Cattaneo
R, Rose JK: Cell fusion by the envelope glycoproteins of persistent measles viruses which caused lethal human brain disease. I Viral 1993, 67:1493-l 502.
23. ..
Baczko K, Lampe J, Lieben V, Pardowitz I, Budka H,
Clonal brain.
expansion virology
UC, Brinckmann U, ter Meulen Cosby SL, lssene S, Rima BK:
of hypermutated 1993,
197:18&195.
measles
virus
in a SSPE
900
Gnomes
and evolution
These autho’rs were in the exceptional position of being able to study five different parts of a brain of a child who died with an NV-induced neurodegenerative disease. Analysis of > 70 matrix cDNA clones revealed that at least four hypermutation events occurred, and that one of the hypermutated viruses had taken over the entire brain by expanding clonally. 24.
Rebagliati
ized . 2s.
MR,
frog
48S99-605.
Bass
BL, Weintraub
RNA
Biol
1990,
activity
48:607413.
44.
Kim
RNA unwinding and modiiing in primary tissues and cell
activity is lines. MO/
Semin
activity:
fact
and
K: Double-stranded RNA adenosine deamimammaliin RNA editing factor. Semin Cell
U, Nishikura
nase as a potential
30.
B, Kohler
M, Sprengel
R, Seeburg
brain controls a determinant of ion flow channels. Ce// 1991, 67~11-19. 31. .
Higuchi M, Single FN, bum PH: RNA editinn
Kohler
M, Sommer
of AMPA structure
PH: RNA
editing in glutamate-gated
8, Sprengel
in
R, See-
370. This paper strengthens the case that ‘A-&’ editing of mRNA encoding glutamate receptor subunits occurs by a mechanism in which the RNA editing substrate has a double-stranded conformation. Thus, this type of editing might indeed be attributable to the dsRNA adenosine deaminase. 32.
33.
Cattaneo R: RNA duplexes 1994, 4:134-l 36.
covalent growth 34.
Saccomanno
.
contains a factor that adenosine to inosine 14:5425-5432.
A factor, injected whether
guide
base conversions.
Curr
Bio/
D, Kinchner MW: An antisense mRNA directs the modiication of the transcript encoding fibrobtast factor in Xenopus oocytes. Cell 1990, 59:687-696.
Kimelman
L, Bass
Lamb 1989,
36.
Weissmann
37.
Morrissey
RNA
C: Sir&-strand LM,
Kirkegaard
modification
activity
with
RNA.
Nafure
Regulation in human cells. K:
RF, Bass BL: Purification
Hough
stranded
RNA
adenosine
a vengeance. 1989,
Nature
337~41 S-41 6.
of double-stranded MO/ Cell Biol 1991,
of the Xenopus faevis doubledeaminase. 1 Biol Chem 1994,
2699933-9939. 39.
Kim U, Garner
TL, Sanford
T, Speicher
K: Purification and characterization adenosine deaminase from bovine Chem 40.
1994,
O’Connell
stranded 41. .
Proc
Nat/
Kim
U,
26913480-l M, Keller
RNA-specific Acad Wang
Sci USA
cloninR of cDNA inase, > candidate Sci
USA
1994,
47.
48.
D, Murray
49.
1994,
recombination in RNA 176:21-32.
Hepatitis replication.
delta virus: Cell 1990,
JL, Bergmann
1992,
Zheng
Fu TB,
of
Lazinski
human
cis and
Top
Warts functions
re-
61:371-373.
Netter
HJ, Bichko
replication 1994,
Sharma
PM,
S: RNA
editing Dev
J: Editing
Taylor
delta
V, Lazinski
cycle
of
virus.
on the geI viral 1992, J: RNA
D, Taylor
human
hepatitis
editvirus.
delta
in press.
Bowman
M,
Madden
in the Wlms’
1994,
Navaratnam T, Giannoni
D,
hepatitis
SL, Rauscher
tumor
FJ, Sukumar
susceptibility
gene,
WT1.
8~720-731.
N, Morrison JR, Bhattacharya F, Teng B-B, Davidson NO,
Pathak
S, Pate1 D, Funahashi Scott J: The p27 cat-
B mRNA 1993,
editing
enzyme
268:20709-20712.
of messenger
RNA
editing.
Annu
VK, Temin HM: Broad spectrum of in vivo forward mutations, hypermutations, and mutational hotspots in a retroviral shuttle vector after a single replication cycle: substitutions, frameshit% and hypermutations. Proc Nat/ Acad Sci USA 1990,
87:601
g-6023.
Vartanian
J-P, Meyerhans
recombination, ficiency virus Li Y, Kappes BH: Molecular
A, Asia
JC, Conway
S: Selection, immunode-
B, Wain-Hobson
and C/A hypermutation type I genomes. / Wrol JA,
of human 1991,
Price
65:1779-l
RW,
Shaw
788.
JM,
Hahn
characterization of human immunodeficiency virus type 1 cloned directly from uncultured human brain tissue: identification of replication-competent and defective viral genomes. ) viral 1991, 65:3973-3985.
5s. ..
Schiff LA, Fields Virology. Edited 199&l 275-l 306. Felder M-P, Laugier M: Functional and
BN: Reoviruses by Fields BN. D, Yatsula
and
their
New
York:
B, Derek%
replication. Raven
P, Calothv
In Press;
G, Marx
biological properties of an avian variant long terminal repeat containing multiple A to C conversions in the U3 sequence. 1 Viral 1994, 6tI4759-4767.
The first demonstration of biased hypermutation in a retroviral genome. Remarkably, this hypermutation event is strictly confined to the U3 region, in which about half of the As are mutated to Gs. It is possible that initially a larger region of a co-replicating retroviral genome was modified, and that the U3 region was transferred successively to the lytic mutant by recombination. 56.
Sharmeen
Tat-dependent tansactivation
RNA 1 Biol
Curr
TL, Cerin JL: Structural requirein hepatitis delta virus: evidence for editing mechanism. Proc Nat/ Acad Sci
51.
53.
viruses.
KF, Brown
editing
Cattaneo R: Different types Rev Cenet 1991, 25:7i-aa.
52.
pop 1992,
89:7149-7153.
H,
Wu T-T,
virus
lmmunol
1992,
50.
JM, Nishikura
of double-stranded nuclear extracts.
3489.
L, Bass B, Sonenberg
N, Weintraub
adenosine-to-inosine modification response RNA. Proc Nat/ Acad
H, Groudine
M:
of wild-type Sci USA
1991,
8a:ao96-8100. 57.
D, Lim B-U, Kang CY: Molecular characterization of the M genomic segment of the Seoul 80-39 virus; nucleotide and amino acid sequence comparisons with other hantaviruses reveal the evolutionary pathway. Virus Res 1991, 19:47-58.
Antic
in press.
T, Zeng
for double-stranded enzyme for RNA in press.
Casey
Genes
W: Purification and properties of doubleadenosine deaminase from calf thymus.
Y, Sanford
for
nomic RNA 66:4693-4697.
54.
11:3719-3725. 38.
46.
cytoplasm of Xenopus oocytes protects double-stranded RNA from modification. MO/ Cell Biol 1994,
C: Unwinding
RA, Dreyfuss 337:19-20.
JM:
quired
ments for RNA a uridine-to-cytidine
BL: The
probably a cytoplasmic dsRNA-binding protein, protects microduplex RNA from deamination. These studies raise the issue of all dsRNA-binding proteins share endogenous substrates.
3s.
Taylor
RNA
JC, Steinhauer D: Curr Top Microbial
alytic subunit of the apolipoprotein is a cytidine deaminase. J Biol Chem
receptor subunit CIuR-B: a determines position and ef-
baskpaired intron ex& ficiency. Cell 1993, 75:1361-l
Genetic
Biochimie
K, Yoo C, Kim U, Murray JM, Estes PA, Cash FE, SA: Substrate specificity of the dsRNA unwinding/modifying enzyme. EM80 1 1991, l&3523-3532.
La Torre
lmmunol
ing in the
Nishikura Liebhaber Sommer
JJ, De
Lai MMC: Microbial
USA
dsRNA unwinding/modifying Dev Biol 1992, 3:42S-433.
. Biol 1993, 4285-293. This and 1271 are excellent reviews of the dsRNA adenosine deaminase by Kazuko Nishikura and Brenda Bass, the two mothers of this enzyme.
29.
4s.
io:ssa6-5590.
BL: The
Bass
fiction. 28. .
regulated
Holland
ulations as quasispecies. 176: l-20. 43.
A developmentally duplexes. Cell 1987,
Wagner RW, Yoo C, Wrabetz L, Kamholz J, Buchhalter J, Hassan NF, Khalili b, Kim SU, Perussia B, McMorris FA, Nishikura
Cell
42.
RNA injections in fertilunwinding activity. Cell
H:
K: Double-stranded detected ubiquitously 27.
DA:
eggs reveal
1987,
that’unwinds 26.
Antisense an RNA duplex
Melton
The dsRNA adenosine deaminase contains three repeats of a dsRNAbinding motif and sequences conserved in the catalytic centre of other deaminases, including a cytidine deaminase involved in apolipoprotein B RNA editing 1491.
K: Molecular RNA adenosine deamediting. Proc Nat/ Acad
Y, Nishikura
R
Cattaneo,
HGnggerberg,
lnstitut f%r Molekularbiologie 8093 Ziirich, Switzerland.
I. Universidt
Ziirich,