TY - JOUR TI - Stem-loop structure in the 5 ' region of potato virus X genome required for plus-strand RNA accumulation AU - Miller, ED AU - Plante, CA AU - Kim, KH AU - Brown, JW AU - Hemenway, C T2 - JOURNAL OF MOLECULAR BIOLOGY AB - Computer-generated thermodynamic predictions and solution structure probing indicated two stem-loop structures, stem-loop 1 (SL1; nt 32-106) and stem-loop 2 (SL2; nt 143-183), within the 5′ 230 nt of potato virus X (PVX) RNA. Because the existence of SL1 was further supported by covariation analysis of several PVX strains, the functional significance of this structure was investigated by site-directed mutational analysis in a tobacco protoplast system. In general, mutations that reduced genomic plus-strand RNA accumulation similarly affected coat protein accumulation, indicating that subgenomic plus-strand RNA was also affected. In contrast, minus-strand RNA levels remained relatively unchanged. Mutational analysis of the stem C (SC) region of SL1 indicated that pairing was more important than sequence, which was consistent with the covariation analysis. Alterations that increased length and stability of either SC or stem D (SD) were deleterious to plus-strand RNA accumulation. The formation of internal loop C between SC and SD, as well as specific nucleotides within this loop, were also required. Several modifications were made to the terminal GAAA tetraloop, a motif known for enhanced RNA stability. Both GANA and GAAG motifs resulted in wild-type levels of RNA accumulation. However, a UUCG tetraloop was detrimental, indicating that the sequence of this element was important beyond just providing stabilization of the structure. These data indicate that multiple features of SL1 are critical for accumulation of PVX plus-strand RNA. DA - 1998/12/4/ PY - 1998/12/4/ DO - 10.1006/jmbi.1998.2174 VL - 284 IS - 3 SP - 591-608 SN - 1089-8638 KW - RNA structure KW - RNA virus KW - RNA replication KW - potato virus X KW - stem-loop ER - TY - JOUR TI - Evolutionary variation in bacterial RNase P RNAs AU - Haas, ES AU - Brown, JW T2 - NUCLEIC ACIDS RESEARCH AB - Sequences encoding RNase P RNAs from representatives of the last remaining classical phyla of Bacteria have been determined, completing a general phylogenetic survey of RNase P RNA sequence and structure. This broad sampling of RNase P RNAs allows some refinement of the secondary structure, and reveals patterns in the evolutionary variation of sequences and secondary structures. Although the sequences range from 100 to <25% identical to one another, and although only 40 of the nucleotides are invariant, there is considerable conservation of the underlying core of the RNA sequence. RNase P RNAs, like group I intron RNAs but unlike ribosomal RNAs, transfer RNAs or other highly conserved RNAs, are quite variable in secondary structure outside of this conserved structural core. Conservative regions of the RNA evolve by substitution of apparently interchangeable alternative structures, rather than the insertion and deletion of helical elements that occurs in the more variable regions of the RNA. In a remarkable case of convergent molecular evolution, most of the unusual structural elements of type B RNase P RNAs of the low G+C Gram-positive Bacteria have evolved independently in Thermomicrobium roseum , a member of the green non-sulfur Bacteria. DA - 1998/9/15/ PY - 1998/9/15/ DO - 10.1093/nar/26.18.4093 VL - 26 IS - 18 SP - 4093-4099 SN - 0305-1048 ER - TY - JOUR TI - The Ribonuclease P Database AU - Brown, JW T2 - NUCLEIC ACIDS RESEARCH AB - Ribonuclease P is responsible for the 5′-maturation of tRNA precursors. Ribonuclease P is a ribonucleoprotein, and in bacteria the RNA subunit alone is catalytically active in vitro , i.e., it is a ribozyme. The Ribonuclease P Database is a compilation of ribonuclease P sequences, sequence alignments, secondary structures, three-dimensional models and accessory information, available via the World Wide Web ( http://www.mbio.ncsu.edu/RNaseP/home.html ). DA - 1998/1/1/ PY - 1998/1/1/ DO - 10.1093/nar/26.1.351 VL - 26 IS - 1 SP - 351-352 SN - 0305-1048 ER -