DELETION MAPPING OF A MOUSE HEPATITIS-VIRUS DEFECTIVE INTERFERING RNAREVEALS THE REQUIREMENT OF AN INTERNAL AND DISCONTIGUOUS SEQUENCE FORREPLICATION

All of the defective interfering (DI) RNAs of mouse hepatitis virus (M HV) contain both the 5' and 3' ends of the viral genomic RNA, which pr esumably include the cis sequences required for RNA replication. To de fine the replication signal of MRV RNA, we have used a vaccinia virus- T7 polymerase-transcribed MHV DI RNA to study the effects of sequence deletion on DI RNA replication. Following infection of susceptible cel ls with a recombinant vaccinia virus expressing T7 RNA polymerase, var ious cDNA clones derived from a DI RNA (DIssF) of the JHM strain of MH V, which is a 3.5-kb naturally occurring DI RNA, behind a T7 promoter were transfected. On superinfection with a helper MHV, the ability of various DI RNAs to replicate was determined. Serial deletions from the middle of the RNA toward both the 5' and 3' ends demonstrated that 85 9 nucleotides from the 5' end and 436 nucleotides from the 3' end of t he MHV RNA genome were necessary for RNA replication. Surprisingly, an additional stretch of 135 nucleotides located at 3.1 to 3.3 kb from t he 5' end of the genome was also required. This stretch is discontiguo us from the 5'-end cis replication signal and is present in all of the naturally occurring DI RNAs studied so far. The requirement for a lon g stretch of 5'- and 3'-end sequences predicts that the subgenomic MHV mRNAs cannot replicate. The efficiency of RNA replication varied with different cDNA constructs, suggesting possible interaction between di fferent regions of DI RNA. The identification of MHV RNA replication s ignals allowed the construction of an MHV DI-based expression vector, which can express foreign genes, such as the chloramphenicol acetyltra nsferase gene.