Tuesday, February 20, 2007 - 22:19
Grasses at Yellowstone National Park are able to grow temperatures (65°; C) that would toast most living things. Step right up! Watch original research, as it happens, on the web! I'm going to use bioinformatics to see if I can find that answer to the puzzle of heat-tolerant plants. Previous parts:
- Part IV: Did we get lost in translation?
Sequence analysis revealed that each of the two RNA segments contains two open reading frames (ORFs) (fig. S2). The 2.2-kb fragment (RNA 1) is involved in virus replication, as both of its ORFs are similar to viral replicases. The first, ORF1a, has 29% amino acid sequence identity with a putative RNA-dependent RNA polymerase (RdRp) from the rabbit hemorrhagic disease virus. The amino acid sequence of the second, ORF1b, has 33% identity with the RdRp of a virus of the fungal pathogen Discula destructiva. These two ORFs overlap and could be expressed as a single protein by frameshifting, a common expression strategy of viral replicases. The two ORFs of RNA 2 have no similarity to any protein with known function. As in most dsRNA mycoviruses, the 5' ends (21 bp) of both RNAs are conserved.I was intrigued by RNA 2 and the identity of the two unidentified open reading frames. What could they be? Like many papers that include sequence analysis, the authors didn't give any information about the searches they did or why they arrived at this conclusion. So, I thought I'd begin by trying to reproduce their results with RNA 2. I got the nucleotide sequence accession numbers from their paper and used blastp to search the nr (non-redundant) protein database at the NCBI with each of the predicted protein sequences.
The second protein didn't give me any significant matches. This probably why the researchers stopped searching and let the story end there. Not me, though. Not only do I have homework to grade, I know other ways to search. Where's the rest of the story? Continue and see. Reference: Márquez, L., et. al. 2007 A Virus in a Fungus in a Plant: Three-Way Symbiosis Required for Thermal Tolerance Science 26: 513-515.
Results from a blastp search with the second ORF