Arterivirus discontinuous mRNA transcription is guided by base pairing between sense and antisense transcription-regulating sequences

Arterivirus discontinuous mRNA transcription is guided by base pairing between sense and antisense transcription-regulating sequences

^*Department of Virology, Leiden University Medical Center, Leiden, The Netherlands; and ^†Section Theoretical Biology and Phylogenetics, Institute of Evolutionary and Ecological Sciences, and Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands

Edited by Paul Ahlquist, University of Wisconsin, Madison, WI, and approved August 6, 1999 (received for review June 8, 1999)

Abstract

To generate an extensive set of subgenomic (sg) mRNAs, nidoviruses (arteriviruses and coronaviruses) use a mechanism of discontinuous transcription. During this process, mRNAs are generated that represent the genomic 5′ sequence, the so-called leader RNA, fused at specific positions to different 3′ regions of the genome. The fusion of the leader to the mRNA bodies occurs at a short, conserved sequence element, the transcription-regulating sequence (TRS), which precedes every transcription unit in the genome and is also present at the 3′ end of the leader sequence. Here, we have used site-directed mutagenesis of the infectious cDNA clone of the arterivirus equine arteritis virus to show that sg mRNA synthesis requires a base-pairing interaction between the leader TRS and the complement of a body TRS in the viral negative strand. Mutagenesis of the body TRS of equine arteritis virus RNA7 reduced sg RNA7 transcription severely or abolished it completely. Mutations in the leader TRS dramatically influenced the synthesis of all sg mRNAs. The construction of double mutants in which a mutant leader TRS was combined with the corresponding mutant RNA7 body TRS resulted in the specific restoration of mRNA7 synthesis. The analysis of the mRNA leader–body junctions of a number of mutants with partial transcriptional activity provided support for a mechanism of discontinuous minus-strand transcription that resembles similarity-assisted, copy-choice RNA recombination.

Footnotes

↵ ‡ Present address: National Institute of Public Health and the Environment, Bilthoven, The Netherlands.
↵ § To whom reprint requests should be addressed at: Department of Virology, Leiden University Medical Center, LUMC P4-26, P.O. Box 9600, 2300 RC, Leiden, The Netherlands. E-mail: Snijder{at}virology.azl.nl.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations:

BHK,

baby hamster kidney;

EAV,

equine arteritis virus;

GL,

large glycoprotein;

i.c.,

intracellular;

IFA,

immunofluorescence assay;

N,

nucleocapsid protein;

nsp,

nonstructural protein;

(+)RNA,

positive-stranded RNA;

RdRp,

RNA-dependent RNA polymerase;

RT-PCR,

reverse transcription–PCR;

sg,

subgenomic;

TRS,

transcription-regulating sequence.