No abstract

We have previously identified a functionally essential bulged stem-loop in the 3 untranslated region of the positive-stranded RNA genome of mouse hepatitis virus. This 68-nucleotide structure is composed of six stem segments interrupted by five bulges, and its structure, but not its primary sequence, is entirely conserved in the related bovine coronavirus. The functional importance of individual stem segments of this stem-loop was characterized by genetic analysis using targeted RNA recombination. We also examined the effects of stem segment mutations on the replication of mouse hepatitis virus defective interfering RNAs. These studies were complemented by enzymatic and chemical probing of the stem-loop. Taken together, our results confirmed most of the previously proposed structure, but they revealed that the terminal loop and an internal loop are larger than originally thought. Three of the stem segments were found to be essential for viral replication. Further, our results suggest that the stem segment at the base of the stem-loop is an alternative base-pairing structure for part of a downstream, and partially overlapping, RNA pseudoknot that has recently been shown to be necessary for bovine coronavirus replication.Mouse hepatitis virus (MHV), one of the best-characterized members of the coronavirus family, has a single-stranded, positive-sense RNA genome some 31 kb in length. Upon infection, the first two-thirds of this exceptional molecule is translated into an RNA-dependent RNA polymerase. Coronavirus RNA synthesis then proceeds by a unique and incompletely understood mechanism described by conflicting models (1, 16, 24, 44-46, 54, 55, 60). Initially, the genomic RNA becomes the template for, at the least, a full-length (negative-sense) antigenome. Further events produce a series of smaller, subgenomic RNAs of both polarities. The positive-sense subgenomic RNAs form a 3Ј nested set, with each containing a 70-nucleotide (nt) leader that is identical to the 5Ј end of the genome and is joined at a downstream site to a stretch of sequence identical to the 3Ј end of the genome. The negativesense subgenomic RNAs form a 5Ј nested set and are roughly 1/10 to 1/100 as abundant as their positive-sense counterparts, with each possessing the complement of this arrangement, including a 5Ј oligo(U) tract and a 3Ј antileader (10, 47).Many advances in investigating the mechanism of coronavirus RNA synthesis have been enabled by the discovery of defective interfering (DI) RNAs of MHV (29, 30, 52) and of other coronaviruses (5,34,39). DI RNAs are extensively deleted genomic remnants that replicate by using the RNA synthesis machinery of a helper virus, often interfering with viral genomic RNA replication. Studies of naturally occurring and artificially constructed DI RNAs, which can be transfected into helper virus-infected cells, have mapped cis-acting sequence elements from the genome that participate in replication and transcription. These deletion analyses have demonstrated that the minimal extent of the 3Ј terminus o...

Classical yeast genetics coupled with the cloning of regulatory genes by complementation of function is a powerful means of identifying and isolating trans-acting regulatory elements. One such regulatory gene is ADR1 which encodes a protein required for transcriptional activation of the glucose-repressible alcohol dehydrogenase (ADH2) gene. We now report the nucleotide sequence of ADR1; it encodes a polypeptide chain of 1,323 amino acids, of which the amino-terminal 302 amino acids are sufficient to stimulate ADH2 transcription. This active amino-terminal region shows amino-acid sequence homology with the repetitive DNA-binding domain of TFIIIA, an RNA polymerase III transcription factor of Xenopus laevis. Similar domains are found in proteins encoded at the Krüppel and Serendipity loci of Drosophila melanogaster. We discuss the implications of this structural homology and suggest that a similar domain may exist in other yeast regulatory proteins such as those encoded by GAL4 (ref. 13) and PPR1 (ref.14).

This manuscript provides nomenclature recommendations developed by an international workgroup to increase transparency and standardization of pharmacogenetic (PGx) result reporting. Presently, sequence variants identified by PGx tests are described using different nomenclature systems. In addition, PGx analysis may detect different sets of variants for each gene, which can affect interpretation of results. This practice has caused confusion and may thereby impede the adoption of clinical PGx testing. Standardization is critical to move PGx forward.