Replication of plus-stranded RNA viruses is greatly affected by numerous host-encoded proteins that act as restriction factors. Cyclophilins, which are a large family of cellular prolyl isomerases, have been found to inhibit Tomato bushy stunt tombusvirus (TBSV) replication in a Saccharomyces cerevisiae model based on genome-wide screens and global proteomics approaches. In this report, we further characterize single-domain cyclophilins, including the mammalian cyclophilin A and plant Roc1 and Roc2, which are orthologs of the yeast Cpr1p cyclophilin, a known inhibitor of TBSV replication in yeast. We found that recombinant CypA, Roc1, and Roc2 strongly inhibited TBSV replication in a cell-free replication assay. Additional in vitro studies revealed that CypA, Roc1, and Roc2 cyclophilins bound to the viral replication proteins, and CypA and Roc1 also bound to the viral RNA. These interactions led to inhibition of viral RNA recruitment, the assembly of the viral replicase complex, and viral RNA synthesis. A catalytically inactive mutant of CypA was also able to inhibit TBSV replication in vitro due to binding to the replication proteins and the viral RNA. Overexpression of CypA and its mutant in yeast or plant leaves led to inhibition of tombusvirus replication, confirming that CypA is a restriction factor for TBSV. Overall, the current work has revealed a regulatory role for the cytosolic single-domain Cpr1-like cyclophilins in RNA virus replication. Among the identified host factors, there are numerous inhibitory host proteins that serve as restriction factors for (ϩ)RNA viruses. However, the functions of the majority of these host proteins during (ϩ)RNA virus replication have not been fully revealed. The restriction factors likely interfere with the viral replication process, which takes place in membrane-bound viral replicase complexes (VRCs) in the cytoplasm of infected cells. The restriction factors potentially target the viral replication proteins, the viral RNA, or host-encoded proteins usurped by (ϩ)RNA viruses to aid the replication process (10-19).Recently, a major effort to dissect host restriction factors has been conducted with TBSV, which is a small (ϩ)RNA virus that is used as a model virus to study virus replication, recombination, and virus-host interactions, based on a yeast (Saccharomyces cerevisiae) model host (20-25). Genome-wide screens of yeast genes and global proteomics approaches have led to the identification of over 500 host genes/proteins that affect TBSV replication or recombination or interact with the viral replication proteins or viral RNA (1, 3, 24-32). Interestingly, ϳ25% of the identified factors seem to inhibit TBSV replication or recombination, suggesting that many host proteins might work as intrinsic restriction factors.The tombusvirus VRC consists of two viral replication proteins (p33 and p92 pol ) and ϳ10 host proteins (18,30,31,33). The auxiliary p33 replication protein is an RNA chaperone involved in recruitment of TBSV (ϩ)RNA to the site of replication, which is the c...