Table 1.

Partial list of structurally polycistronic viral mRNAs which are functionally monocistronic, i.e. only the first cistron is translated^a

Virus	Expressed 5′ cistronb	Silent 3′ cistron(s)	Source of short transcriptc	References
Polyoma virus	Capsid protein VP2	Capsid protein VP1	Splicing	Siddell and Smith, 1978
Bovine papillomavirus	Numerous examples	Numerous examples	Promoter switch and splicing	Lambert et al., 1988
Cytomegalovirus	UL98d	UL99 (pp28)	Promoter switch	Wing and Huang, 1995
Adenovirus	Numerous examples	Numerous examples	Splicing	Wold et al., 1995, Ziff, 1985
Parvovirus: adeno-associated	Capsid protein A	Capsid proteins B/C	Splicing	Muralidhar et al., 1994
Hepatitis B virus	Core protein	S proteins (envelope)	Promoter switch	Schaller and Fischer, 1991
Retrovirus: avian, murine	Gag (capsid) protein	Env protein	Splicinge	Pawson et al., 1977, Van Zaane et al., 1977
Retrovirus: human foamy	Gag (capsid) protein	Pol precursor	Splicing	Jordan et al., 1996
Lentivirus: HIV-1	Tat	Rev and Neff	Splicing	Schwartz et al., 1992
Alphavirus: Semliki Forest	Nonstructural proteins	Capsid protein	Internal promoter	Glanville et al., 1976, Strauss and Strauss, 1994
Calicivirus: felineg	Nonstructural proteins	Capsid protein	Independent replication	Carter, 1990, Neill et al., 1991
Coronavirus: mouse hepatitis	Membrane protein	Nucleocapsid protein	Discontinuous transcription	Lai and Cavanagh, 1997
Equine arteritis virus	Replicase polyprotein	Gs glycoprotein	Discontinuous transcription	Pasternak et al., 2000
Brome mosaic virus	RNA polymerase	Coat protein	Internal promoter	Miller et al., 1985, Shih and Kaesberg, 1976
Tobacco mosaic virus	Replicase	Coat and movement proteins	Internal promoters	Grdzelishvili et al., 2000, Hunter et al., 1976
Potato virus X	25 kDa movement protein	12 and 8 kDa movement proteinsf	??	Verchot et al., 1998
Carmovirus: turnip crinkleg	Replicase (p28/p88)	p8 and p9 movement proteins	Internal promoters	Li et al., 1998, Wang and Simon, 1997
Tombusvirus: tobacco necrosisg	RNA polymerase	Coat protein (ORF5)h	Internal promoters?	Meulewaeter et al., 1992
Southern bean mosaic virusg	Movement protein and polymerasef	Coat protein	Internal promoter	Hacker and Sivakumaran, 1997
Luteovirus: barley yellow dwarfg	Protease/polymerase	Coat protein and p17f	Internal promoters	Koev and Miller, 2000, Mayo and Ziegler-Graff, 1996
Turnip yellow mosaic tymovirus	p69 and p206 replicasef	Coat protein	Internal promoter	Schirawski et al., 2000, Szybiak et al., 1978
Closterovirus: citrus tristeza; beet yellows	Polymerase precursor	Eight to ten downstream ORFs	Internal transcription elements	Gowda et al., 2001, Peremyslov and Dolja, 2002
Geminivirus: tomato leaf curl	C1 replication proteind	C2 transcription factor	Internal promoter	Mullineaux et al., 1993
Pararetrovirus: rice tungro bacilliform	ORFs 1, 2, 3f	ORF4	Splicing	Fütterer et al., 1994

The silent downstream cistron is expressed only upon being moved closer to the 5′ end via production of a second, shorter mRNA.

^aTranslation of most genes derived from these viruses follows straightforward predictions of the scanning mechanism, although occasional deviations have been reported. In rare instances where a 3′ cistron appears to be translated from a dicistronic mRNA (Grundhoff and Ganem, 2001, Kirshner et al., 1999, Nador et al., 2001, Stacey et al., 2000), the virus in question employs a complicated pattern of splicing and therefore the existence of an undetected monocistronic mRNA is not beyond the realm of reason. In some other cases only a small amount of the protein encoded by the 3′ cistron was produced, and the published RNA analyses were not sufficiently sensitive to rule out the presence of an additional subgenomic mRNA (Herbert et al., 1996).

^bIn some cases the listed example is arbitrary, i.e. with retroviruses, coronaviruses, closteroviruses, etc., there are additional polycistronic mRNAs wherein translation is restricted to the 5′ cistron.

^cWhereas DNA viruses and retroviruses use conventional promoter-switching or splicing mechanisms to generate alternative forms of mRNA that allow translation of the downstream cistron, more complicated mechanisms underlie the production of subgenomic mRNAs by some RNA viruses (Miller and Koev, 2000).

^dThe presence of internal promoters that produce a shorter transcript for each downstream ORF is suggestive, but testing of translation is still needed for the mRNAs produced by cytomegalovirus and geminivirus.

^eWhereas all retroviruses employ splicing to produce the subgenomic mRNA from which envelope protein (Env) is translated, some retroviruses also employ an internal promoter which is postulated to mediate expression of novel ORFs, such as the superantigen of mouse mammary tumor virus (Reuss and Coffin, 1998) and orf-x of the virus that causes lung cancer in sheep (Palmarini et al., 2002).

^fSee leaky scanning in Table 3 and Fig. 1.

^gIn place of the usual m7G cap, the 5′ end of these viral RNAs carries a covalently linked protein (VPg) or is unblocked. The need for a subgenomic mRNA even in these cases emphasizes that translation is 5′ end-dependent even when it is not cap-dependent.

^hThe full-length genomic mRNA supports translation of the 3′ cistron in vitro but the 3′ cistron is silent in vivo. The latter result is considered more reliable (Meulewaeter et al., 1992).