Leaky scanning


Leaky scanning is a phenomenon in which a weak initiation codon triplet on the mRNA is sometimes skipped by the ribosome during translation initiation. The ribosomal subunit 40S continues scanning to another initiation codon. The weak initiation codon can be an ACG or an ATG in a weak Kozak consensus context.
In this way, one mRNA can code for several different proteins if the AUG are not in frame, or for proteins with different N-termini if the AUG are in the same frame.

Upstream ORFs (uORF) are small coding regions preceding an ORF, The latter must be translated by leaky scanning or termination-reinitiation. Many eukaryotic genes encode for uORF to downregulate the translation/mRNA ratio of a gene. These genes are described in the uORF database
The leaky scanning is favored in case of cellular stress in which EIF2alpha is phosphorylated , like in case of dsRNA/PKR activation. Many eukaryotic stress response genes are under the transcription control of a uORF. Viruses may use this regulatory system for their own purpose.

Family Host Genus Virus Products RefSeq Ref.
Bunyaviridae image Orthobunyavirus Bunyamwera virus NS/NSs NC_001927
image Hantavirus Andes virus NS/NSs NC_003466
image Phlebovirus Rift valley fever virus NSm-Gn, NSm, NSm' NC_014396
Caliciviridae image Norovirus Murine norovirus ORF4/CP NC_008311
Hepadnaviridae image Orthohepadnavirus Hepatitis B virus HBeAg/C/P NC_003977
M/S? NC_003977
Hepeviridae image Hepevirus Hepatitis E virus ORF3/CP NC_001434
Herpesviridae image Simplexvirus Human herpesvirus 1 uORF/UL30 NC_001806
image Cytomegalovirus Human cytomegalovirus uORF2/gp74 NC_006273
image Rhadinovirus Kaposi's sarcoma-associated herpesvirus uORF1+ORF35/
Orthomyxoviridae image Influenza virus A A/Puerto Rico/8/34 PB1/PN1-F2/N40 NC_002021
image Influenza virus B B/Lee/1940 NB/NA NC_002209
Papillomaviridae image Alphapapillomavirus HPV16 E6/E7 NC_001526
Polyomaviridae image Polyomavirus SV40 Agno/VP2/VP3? NC_001669
Paramyxoviridae image Aquaparamyxovirus Sendai virus P/C EU156171
image Respirovirus Sendai virus C'/P/C/Y1/Y2 NC_001552
image Morbilivirus Measles virus P/C NC_001498
image Henipavirus Hendra virus P/C NC_001906
Reoviridae image Rotavirus Rotavirus A VP7.1/VP7.2, NC_011503
NSP5/NSP6 NC_011505
image Orbivirus Bluetongue virus Vp6a, NS4 NC_006008
NS3a NC_006015
image Orthoreovirus Mammalian orthoreovirus Sigma1/sigma1s NC_004277
MuNS/MuNSC NC_004281
Coronaviridae image Betacoronavirus Bovine coronavirus N/I NC_003045
Arteriviridae image Arterivirus Equine arteritis virus E/GP2 NC_002532
ORF5a/GP5 NC_002532
Alphatetraviridae image Omegatetravirus Helicoverpa armigera stunt virus P17/CP NC_004060
Baculoviridae image Alphabaculovirus Autographa californica multiple nucleopolyhedrovirus uORF/gp64 NC_004323
Alphaflexviridae image Potexvirus Potato virus X TGB2/TGB3 NC_011620
Caulimoviridae image Tungrovirus Rice tungro bacilliform virus ORF1/ORF2/ORF3 NC_001914
Luteoviridae image Luteovirus Barley yellow dwarf virus P3a/CP/MP NC_004750
image Polerovirus Potato leafroll virus P0/P1 NC_001747
P3a/CP/MP NC_001747
image Enamovirus Pea enation mosaic virus P0/P1 NC_003629
Tombusviridae image Aureusvirus Pothos latent virus MP/P14 NC_000939
image Machlomovirus Maize chlorotic mottle virus ORF1/ORF2 NC_003627
Unassigned image Sobemovirus Southern bean mosaic virus MP/X/ORF2A NC_004060
Tymoviridae image Tymovirus Turnip yellow mosaic virus MVP/ORF1 NC_004063
Virgaviridae image Hordeivirus Barley stripe mosaic virus TGB2/TGB3 NC_003481
image Pecluvirus Peanut clump virus CP/P39 NC_003668