RNA Secondary Structure Of Pms3 Which Regulates The Photoperiod-Sensitive Male Sterility In Rice And The Crystal Structure Of Protein RPA3017

The discovery of photo-sensitive genic male sterile(PSMS) rice Nongken 58 S, which was complete sterile under long-day conditions and fertile under short-day conditions, was an important resource for two-line hybrids. Many groups have carried out genetic analysis and mapping of the gene that regulates PSMS, finding that pms3 locus was the cause. Studies showed that transcript-1, the candidate gene of pms3, was a long non-coding RNA(lnc RNA). A spontaneous mutation caused a single nucleotide polymorphism(SNP) between the wild-type and mutant. Meanwhile it was found that the transcript-1 didn’t encode proteins, thus its regulatory function might be executed by two ways: one is depending on the mi RNAs it produces to connect with downstream DNA or proteins; the other is depending only on the lnc RNA with its secondary or tertiary structure fold to interact with downstream DNA or proteins. RNA secondary structure can be predicted by software or detected by experiments methods. Here we used several softwares to predict the full-length or truncated transcript-1, and probed the secondary structure of transcript-1 lnc RNA by Selective 2’-Hydroxyl Acylation analyzed by Primer Extension(SHAPE) to analyze how the structure characteristics around the SNP, the recognition and the cut sites of mi RNA help to exert its function.Signal transduction in bacterial systems is commonly mediated by two-component systems(TCS) that provoke cellular responses to various environmental signals. Response regulator(RR) is the second component of TCS, in which a conserved aspartic acid residue receives a phosphoryl group from the first component, a phosphorylated histidine kinase(HK). In photosynthetic bacterium R. palustris, photosynthesis at low-light conditions is regulated by two tandem red-light photoreceptorsbacteriophytochromes: Rp Bph P2 and Rp Bph P3. Red-light signals perceived by Rp Bph P2 and Rp Bph P3 alter auto-phosphorylation levels of the C-terminal HK domains, from which the phosphoryl group is further relayed to the same response regulator RPA3017 to mediate downstream cellular responses. To understand how the cognate phosphor-relay between Rp Bph P2/Rp Bph P3 and RPA3017 is achieved at the molecular level, we determined the crystal structure of RPA3017 at 1.8? resolution. RPA3017 adopted a Rossmann fold with a typical(β/α)5 architecture similar to Che Y-type RRs. Based on structural analyses and homology modeling, we identified a surface patch near the phosphor-acceptor Asp70 on RPA3017 that directly interacted with the HK domains in its upstream partners, Rp Bph P2 and Rp Bph P3. This work provided structural insights into how specific recognition between cognate signaling partners in TCS was achieved at the molecular level.