2A is an oligopeptide sequence mediating a ribosome ‘skipping’ effect, producing an apparent ‘cleavage’ of polyproteins. First identified and characterized in picornaviruses, ‘2A-like’ sequences are found in other mammalian viruses and a wide range of insect viruses. Databases were analysed using a motif conserved amongst 2A/2A-like sequences. The newly identified 2A-like sequences (30 aa) were inserted into a reporter polyprotein to determine their cleavage activity. Our analyses showed that these sequences fall into two categories. The majority mediated very high (complete) cleavage to separate proteins and a few sequences mediated cleavage with lower efficiency, generating appreciable levels of the uncleaved form. Phylogenetic analyses of 2A-like sequences and RNA-dependent RNA polymerases (RdRps) indicated multiple, independent, acquisitions of these sequences at different stages during virus evolution. Within a virus family, 2A sequences are (probably) homologous, but diverge due to other evolutionary pressures. Amongst different families, however, 2A/2A-like sequences appear to be homoplasic.
de MirandaJ. R.,
DrebotM.,
TylerS.,
ShenM.,
CameronC. E.,
StoltzD. B.,
CamazineS. M.2004; Complete nucleotide sequence of Kashmir bee virus and comparison with acute bee paralysis virus. J Gen Virol 85:2263–2270[CrossRef]
DonnellyM. L. L.,
LukeG.,
MehrotraA.,
LiX.,
HughesL. E.,
GaniD.,
RyanM. D.2001a; Analysis of aphthovirus 2A/2B polyprotein ‘cleavage’ mechanism indicates not a proteolytic reaction, but a novel translational effect: a putative ribosomal ‘skip’. J Gen Virol 82:1013–1025
DonnellyM. L. L.,
HughesL. E.,
LukeG.,
MendozaH.,
Ten DamE.,
GaniD.,
RyanM. D.2001b; The ‘cleavage’ activities of foot-and-mouth disease virus 2A site-directed mutants and naturally occurring ‘2A-like’ sequences. J Gen Virol 82:1027–1041
GorbalenyaA. E.,
PringleF. M.,
ZeddamJ. L.,
LukeB. T.,
CameronC. E.,
KalmakoffJ.,
HanzlikT. N.,
GordonK. H. J.,
WardV. K.2002; The palm subdomain-based active site is internally permuted in viral RNA-dependent RNA polymerases of an ancient lineage. J Mol Biol 324:47–62[CrossRef]
GovanV. A.,
LeatN.,
AllsoppM.,
DavisonS.2000; Analysis of the complete genome sequence of acute bee paralysis virus shows that it belongs to the novel group of insect-infecting RNA viruses. Virology 277:457–463[CrossRef]
GrahamR. I.,
RaoS.,
PosseeR. D.,
SaitS. M.,
MertensP. P. C.,
HailsR. S.2006; Detection and characterization of three novel species of reovirus ( Reoviridae ), isolated from geographically separate populations of the winter moth Operophtera brumata (Lepidoptera: Geometridae) on Orkney. J Invertebr Pathol 91:79–87[CrossRef]
HeathL.,
van der WaltE.,
VarsaniA.,
MartinD. P.2006; Recombination patterns in aphthoviruses mirror those found in other picornaviruses. J Virol 80:11827–11832[CrossRef]
HughesL.2003; Analysis of the Foot-and-mouth disease virus 2A-mediated polyprotein processing event . PhD thesis University of St Andrews;
IsawaH.,
AsanoS.,
SaharaK.,
IizukaT.,
BandoH.1998; Analysis of genetic information of an insect picorna-like virus, infectious flacherie virus of silkworm: evidence for evolutionary relationships among insects, mammalian and plant picorna(-like) viruses. Arch Virol 143:127–143[CrossRef]
JayaramH.,
EstesM. K.,
PrasadB. V.2004; Emerging themes in rotavirus cell entry, genome organization, transcription and replication. Virus Res 101:67–81[CrossRef]
JonesM. S.,
LukashovV. V.,
GanacR. D.,
SchnurrD. P.2007; Discovery of a novel human picornavirus in a stool sample from a pediatric patient presenting with fever of unknown origin. J Clin Microbiol 45:2144–2150[CrossRef]
KimM. C.,
KwonY. K.,
JohS. J.,
LindbergA. M.,
KwonJ. H.,
KimJ. H.,
KimS. J.2006; Molecular analysis of duck hepatitis virus type 1 reveals a novel lineage close to the genus Parechovirus in the family Picornaviridae . J Gen Virol 87:3307–3316[CrossRef]
LanglandJ. O.,
PettifordS.,
JiangB.,
JacobsB. L.1994; Products of the porcine group C rotavirus NSP3 gene bind specifically to double-stranded RNA and inhibit activation of the interferon-induced protein kinase PKR. J Virol 68:3821–3829
LanziG.,
de MirandaJ. R.,
BoniottiM. B.,
CameronC. E.,
LavazzaA.,
CapucciL.,
CamazineS. M.,
RossiC.2006; Molecular and biological characterization of deformed wing virus of honeybees ( Apis mellifera L.). J Virol 80:4998–5009[CrossRef]
LindbergA. M.,
JohanssonS.2002; Phylogenetic analysis of Ljungan virus and A-2 plaque virus, new members of the Picornaviridae . Virus Res 85:61–70[CrossRef]
MaoriE.,
TanneE.,
SelaI.2007; Reciprocal sequence exchange between non-retro viruses and hosts leading to the appearance of new host phenotypes. Virology 362:342–349[CrossRef]
OemJ. K.,
LeeK. N.,
ChoI. S.,
KyeS. J.,
ParkJ. H.,
JooY. S.2004; Comparison and analysis of the complete nucleotide sequence of foot-and-mouth disease viruses from animals in Korea and other PanAsia strains. Virus Genes 29:63–71[CrossRef]
OngusJ. R.,
PetersD.,
BonmatinJ.-M.,
BengschE.,
VlakJ. M.,
van OersM. M.2004; Complete sequence of a picorna-like virus of the genus Iflavirus replicating in the mite Varroa destructor . J Gen Virol 85:3747–3755[CrossRef]
PironM.,
DelaunayT.,
GrosclaudeJ.,
PoncetD.1999; Identification of the RNA-binding, dimerization, and eIF4GI-binding domains of rotavirus nonstructural protein NSP3. J Virol 73:5411–5421
PoulosB. T.,
TangK. F.,
PantojaC. R.,
BonamiJ. R.,
LightnerD. V.2006; Purification and characterization of infectious myonecrosis virus of penaeid shrimp. J Gen Virol 87:987–996[CrossRef]
PringleF. M.,
JohnsonK. N.,
GoodmanC. L.,
McIntoshA. H.,
BallL. A.2003; Providence virus: a new member of the Tetraviridae that infects cultured insect cells. Virology 306:359–370[CrossRef]
RaoS.,
CarnerG. R.,
ScottS. W.,
OmuraT.,
HagiwaraK.2003; Comparison of the amino acid sequences of RNA-dependent RNA polymerases of cypoviruses in the family Reoviridae . Arch Virol 148:209–219[CrossRef]
RyanM. D.,
DonnellyM. L. L.,
LewisA.,
MehrotraA. P.,
WilkieJ.,
GaniD.1999; A model for non-stoichiometric, co-translational protein scission in eukaryotic ribosomes. Bioorg Chem 27:55–79[CrossRef]
ThompsonJ. D.,
HigginsD. G.,
GibsonT. J.1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680[CrossRef]
ThompsonJ. D.,
GibsonT. J.,
PlewniakF.,
JeanmouginF.,
HigginsD. G.1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882[CrossRef]
TsengC. H.,
KnowlesN. J.,
TsaiH. J.2007; Molecular analysis of duck hepatitis virus type 1 indicates that it should be assigned to a new genus. Virus Res 123:190–203[CrossRef]
VallesS. M.,
StrongC. A.,
DangP. M.,
HunterW. B.,
PereiraR. M.,
OiD. H.,
ShapiroA. M.,
WilliamsD. F.2004; A picorna-like virus from the red imported fire ant, Solenopsis invicta : initial discovery, genome sequence, and characterization. Virology 328:151–157[CrossRef]
van der WilkF.,
DullemansA. M.,
VerbeekM.,
van den HeuvelJ. F. J. M.1997; Nucleotide sequence and genomic organization of Acyrthosiphon pisum virus. Virology 238:353–362[CrossRef]
WangX.,
YhangJ.,
LuJ.,
YiF.,
LiuC.,
HuY.2004; Sequence analysis and genomic organization of a new insect picorna-like virus, Ectropis obliqua picorna-like virus, isolated from Ectropis obliqua . J Gen Virol 85:1145–1151[CrossRef]
WuC. Y.,
LoC. F.,
HuangC. J.,
YuH. T.,
WangC. H.2002; The complete genome sequence of Perina nuda picorna-like virus, an insect-infecting RNA virus with a genome organization similar to that of the mammalian picornaviruses. Virology 294:312–323[CrossRef]
YangH.,
MakeyevE. V.,
KangZ.,
JiS.,
BamfordD. H.,
van DijkA. A.2004; Cloning and sequence analysis of dsRNA segments 5, 6 and 7 of a novel non-group A, B, C adult rotavirus that caused an outbreak of gastroenteritis in China. Virus Res 106:15–26[CrossRef]