Table 3.

Partial list of cellular and viral mRNAs that produce two separately-initiated proteins by context-dependent leaky scanning^a

Source of mRNA	Identifying information	Sequence flanking first AUG codonb	Protein productsc	References
Glucocorticoid receptor gene	Human	CUGaugG; tested	Long and short transactivators	Yudt and Cidlowski, 2001
NFAT transcription factor gene	Human	CGGaugC	90 and 86 kDa isoforms	Lyakh et al., 1997
C/EBPα gened	Mouse	CCCaugG; tested	42 and 30 kDa isoforms	Lin et al., 1993, Ossipow et al., 1993
Rx/rax homeobox gene	Mouse	UCCaugC; tested	Long and short isoforms	Tucker et al., 2001
GATA-1 gene	Human, mouse	CCCaugG (mouse); UCCaugG (human)	50 and 40 kDa isoforms	Calligaris et al., 1995, Wechsler et al., 2002
Peripherin gene	Rat	UGAaugC; tested	Long and short isoforms	Ho et al., 1995
MxB protein gene	Human	CACaugU; tested	Nuclear and cytoplasmic isoforms	Melén et al., 1996
Ubiquitin-activating enzyme E1 gene	Human	UUGaugU	Nuclear and cytoplasmic isoforms	Handley-Gearhart et al., 1994, Shang et al., 2001
Microtubule-associated protein gene	Human	CCAaugC	Long and short isoforms	Su and Qi, 2001
Von Hippel-Lindau genee	Human	GGAaugC	24 and 18 kDa isoforms	Iliopoulos et al., 1998, Schoenfeld et al., 1998
S6 kinase gene	Human, rat	CCCaugA	Long and short isoforms	Grove et al., 1991, Reinhard et al., 1992
Rlk/Txk tyrosine kinase gene	Mouse	GCCaugA	Long and short isoforms	Debnath et al., 1999
Vitamin D receptor gene	Chicken	UCCaugU; tested	Long and short isoforms	Lu et al., 1997
Val-tRNA synthetase gene	Arabidopsis	UCUaugU; tested	Mitochondrial and cytoplasmic isoforms	Souciet et al., 1999
Simian virus 40	Late 19S mRNA	UCCaugG; tested	Capsid proteins VP2 and VP3	Sedman and Mertz, 1988
Cytomegalovirus	UL4 mRNA	GUGaugC; tested	Inhibitory peptide and gp48	Cao and Geballe, 1995
Adenovirus type 5	Region E3	UAUaugA	6.7 kDa protein and gp19K	Wilson-Rawls et al., 1990, Wold et al., 1986
Adenovirus type 5	Region E1B	UCCaugG	21 kDa and 55kDa proteins	Bos et al., 1981
Hepatitis B virus	2.1 kb mRNA	GCCaugC; tested	Middle (pre-S2) and small (p24) surface proteins	Sheu and Lo, 1992
Feline leukemia retrovirusf	Genomic mRNA	CUGaugU	gp80gag and pr65gag	Laprevotte et al., 1984
HIV-1	Spliced mRNA	GUAaugC; tested	Vpu and Env	Schwartz et al., 1992
HIV-1	Spliced mRNA	CCUaugG; tested	Rev and Nef	Schwartz et al., 1992
Reovirus (mammalian)	RNA segment S1	CGGaugG; tested	σ1 and 14kDa proteins	Fajardo and Shatkin, 1990, Kozak, 1982
Reovirus (baboon)g	RNA segment S4	UACaugG	p15 and p16 proteins	Dawe and Duncan, 2002
Bunyavirus	RNA segment S	UCAaugA	Nucleocapsid (N) and NSs	Bridgen et al., 2001, Elliott and McGregor, 1989
Influenza A virusg	RNA segment 2	UGAaugG	Polymerase subunit PB1 and mitochondrialprotein	Chen et al., 2001
Barley yellow dwarf luteovirus	Subgenomic mRNA	UGAaugA; tested	Coat protein and p17	Dinesh-Kumar and Miller, 1993
Turnip yellow mosaic viruse	Genomic mRNA	CAAaugA	p69 and p206replicase	Weiland and Dreher, 1989
Cucumber necrosis virus	0.9 kb subgenomic mRNA	UUCaugG; tested	p21 and p20	Johnston and Rochon, 1996
Peanut clump furovirus	RNA segment 2	CUUaugU; tested	p23 (coat) and p39	Herzog et al., 1995
Potato virus X potexvirus	Subgenomic mRNA	CAUaugU; tested	12 and 8kDa movement proteins	Verchot et al., 1998
Southern bean mosaic virusg	Genomic mRNA	UUUaugA; tested	p21 movement protein and p105polymerase	Sivakumaran and Hacker, 1998
Baculovirusd	IE0 mRNA	GACaugA	Long and short forms of transactivator (IE0, IE1)	Theilmann et al., 2001

^aSome additional examples of leaky scanning are described in Fig. 1, Fig. 2 and in the text.

^bIn all mRNAs here listed, the sequence flanking the first start codon deviates from the consensus sequence in position −3 and/or position +4, highlighted by underlining. When the postulated link between context and leaky scanning was tested (so marked in this column), mutations that improved the context at the first start site diminished access to the downstream start site. This test failed only with cucumber necrosis virus, where the short distance between the m7G cap and AUG#1 allowed some leaky scanning even when the context was optimized.

^cIn some cases the first and second AUG codons are in the same reading frame, generating long and short versions of the encoded protein which may function differently. In cases where the first and second start codons are in different reading frames, indicated by italicizing the second product, the extent of overlap between the two ORFs ranges from a few codons (peanut clump virus, southern bean mosaic virus) to 626 codons (turnip yellow mosaic virus).

^dAccess to the downstream initiation site via leaky scanning is augmented by a reinitiation shunt, as explained in the text (Section 4.3) and diagrammed in Fig. 1 for C/EBPβ mRNA.

^eMutations that eliminate AUG#1 usually increase production of the second, downstream protein. In rare cases where the expected increase was not seen (e.g. von Hippel-Lindau, turnip yellow mosaic virus), it might be because translation of the second protein was restricted at the level of elongation. For a similar reason, improving the context around AUG#1 occasionally fails to elevate production of the protein there initiated (Fajardo and Shatkin, 1990). These entries nevertheless satisfy the main prediction of the leaky scanning mechanism, which is that improving the context around AUG#1 prevents initiation from the second, downstream site (Fajardo and Shatkin, 1990, Iliopoulos et al., 1998).

^fWhereas feline leukemia virus produces an N-terminally-extended, glycosylated form of Gag (gp80^gag) from the indicated weak AUG codon, the corresponding upstream start site in murine leukemia virus is ACCCUGG (Portis et al., 1994). When that site was experimentally ablated, however, revertants expressed the extended protein from a weak upstream AUG codon (UUUaugG) created by a point mutation. Those revertants were selected because the extra glycosylated form of Gag contributes to viral spread (Portis et al., 1996).

^gIn the mRNAs from baboon reovirus, influenza A virus, and southern bean mosaic virus, the indicated proteins derive from the first (weak) and fourth AUG codons. AUG#2 and AUG#3 initiate small ORFs that terminate before AUG#4. Thus, a combination of leaky scanning and reinitiation probably mediates access to the downstream start site.