Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses.

Virology
Andrew E FirthJ F Atkins

Abstract

Flaviviruses have a positive-sense, single-stranded RNA genome of approximately 11 kb, encoding a large polyprotein that is cleaved to produce approximately 10 mature proteins. Cell fusing agent virus, Kamiti River virus, Culex flavivirus and several recently discovered flaviviruses have no known vertebrate host and apparently infect only insects. We present compelling bioinformatic evidence for a 253-295 codon overlapping gene (designated fifo) conserved throughout these insect-specific flaviviruses and immunofluorescent detection of its product. Fifo overlaps the NS2A/NS2B coding sequence in the -1/+2 reading frame and is most likely expressed as a trans-frame fusion protein via ribosomal frameshifting at a conserved GGAUUUY slippery heptanucleotide with 3'-adjacent RNA secondary structure (which stimulates efficient frameshifting in vitro). The discovery bears striking parallels to the recently discovered ribosomal frameshifting site in the NS2A coding sequence of the Japanese encephalitis serogroup of flaviviruses and suggests that programmed ribosomal frameshifting may be more widespread in flaviviruses than currently realized.

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Citations

Nov 25, 2014·Emerging Infectious Diseases·Karin PachlerNorbert Nowotny
Oct 26, 2011·Proceedings of the National Academy of Sciences of the United States of America·Gary LoughranJohn F Atkins
Jul 24, 2012·Molecular Biology and Evolution·Niv SabathDavid Karlin
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Jul 9, 2013·Virology·Roger LingAndrew E Firth
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Jun 22, 2021·Access Microbiology·Kim R BlasdellCadhla Firth

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Datasets Mentioned

BETA
AB262759
GQ165808
FJ644291
AY149904
AB488408
AF411835
AY149905
FJ711167
AY632540
FJ883471

Methods Mentioned

BETA
overprinting
ICE
PCR

Software Mentioned

Illustrator
RDP2
CLUSTALW
ImageQuant
Photoshop
Adobe
MLOGD
NOUV
CLUSTALX
pknotsRG

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