ABSTRACT
Orthologous introns have identical positions relative to the coding sequence in orthologous genes of different species. By analyzing the complete genomes of five plants we generated a database of 40,512 orthologous intron groups of dicotyledonous plants, 28,519 orthologous intron groups of angiosperms, and 15,726 of land plants (moss and angiosperms). Multiple sequence alignments of each orthologous intron group were obtained using the Mafft algorithm. The number of conserved regions in plant introns appeared to be hundreds of times fewer than that in mammals or vertebrates. Approximately three quarters of conserved intronic regions among angiosperms and dicots, in particular, correspond to alternatively-spliced exonic sequences. We registered only a handful of conserved intronic ncRNAs of flowering plants. However, the most evolutionarily conserved intronic region, which is ubiquitous for all plants examined in this study, including moss, possessed multiple structural features of tRNAs, which caused us to classify it as a putative tRNA-like ncRNA. Intronic sequences encoding tRNA-like structures are not unique to plants. Bioinformatics examination of the presence of tRNA inside introns revealed an unusually long-term association of four glycine tRNAs inside the Vac14 gene of fish, amniotes, and mammals.
Subject(s)
Introns , Magnoliopsida/genetics , RNA, Plant , Algorithms , Animals , Arabidopsis/genetics , Arabidopsis/growth & development , Base Sequence , Bryophyta/genetics , Computational Biology/methods , Conserved Sequence , Databases, Genetic , Flowers/genetics , Genome, Plant , Humans , Mice , Molecular Sequence Data , Oryza/genetics , Phylogeny , Populus/genetics , RNA, Plant/chemistry , RNA, Transfer/genetics , Vitis/geneticsABSTRACT
Since soluble silicon (Si) has been shown to alleviate copper (Cu) toxicity in Arabidopsis thaliana, the expression of genes involved in responses to Cu toxicity was examined by quantitative reverse transcription-polymerase chain reaction. Expression levels of three metallothionein (MT) genes were increased under Cu stress conditions whereas Cu-stressed plants treated with Si either maintained high levels or contained even higher levels of MT RNA. Cu/zinc superoxide dismutase (SOD) enzyme activity was induced by Cu toxicity. However, SOD activity was increased even more if plants were provided with extra Si and toxic levels of Cu. Previously, plants treated with elevated Cu showed increased phenylalanine ammonia lyase (PAL) activity that was reduced when the plants were also provided with extra Si. Since the Arabidopsis genome encodes 4 PAL genes (PAL1-4), we examined which ones were responsive to Cu and Si. PAL 1, PAL 2, and PAL 3 all showed similar patterns of gene expression that matched previous enzymatic data while PAL4 was elevated by the presence of high Cu whether Si was present or not. Taken together, these data suggested that Si permitted plants to respond to Cu toxicity more effectively and that these changes occurred at the gene expression level.
Subject(s)
Arabidopsis/drug effects , Arabidopsis/metabolism , Copper/toxicity , Silicon/pharmacology , Arabidopsis/genetics , Arabidopsis Proteins/metabolism , Enzyme Activation/drug effects , Gene Expression Regulation, Plant/drug effects , Metallothionein/metabolism , Phenylalanine Ammonia-Lyase/metabolism , Plant Roots/drug effects , Plant Roots/metabolism , Protein Binding/drug effects , Reverse Transcriptase Polymerase Chain Reaction , Superoxide Dismutase/metabolismABSTRACT
The complete genomic sequence of the Toledo isolate of the comovirus, turnip ringspot virus (TuRSV), was found to consist of 2 polyadenylated RNAs. RNA 1 is 6082 nucleotides long and encodes a single predicted polypeptide of 1860 amino acids. The predicted RNA 1 polyprotein contains the polypeptides for viral replication and proteolytic processing. RNA 2, that is 3985 nucleotides long, codes for a single predicted 1095 amino acid polypeptide containing the movement and coat proteins. Phylogenetic analysis indicates that TuRSV is most closely related to radish mosaic virus, and these crucifer-infecting pathogens form a distinct clade within the comoviruses.
Subject(s)
Brassica napus/virology , Comovirus/genetics , Genome, Viral , Plant Diseases/virology , Sequence Analysis, DNA , Base Sequence , Comovirus/isolation & purification , Comovirus/metabolism , Molecular Sequence Data , Ohio , Polyproteins/chemistry , Polyproteins/genetics , Polyproteins/metabolism , RNA, Viral/genetics , Viral Proteins/chemistry , Viral Proteins/genetics , Viral Proteins/metabolismABSTRACT
Cauliflower mosaic virus (CaMV) gene VI encodes a multifunctional protein (P6) involved in the translation of viral RNA, the formation of inclusion bodies, and the determination of host range. Arabidopsis thaliana ecotype Tsu-0 prevents the systemic spread of most CaMV isolates, including CM1841. However, CaMV isolate W260 overcomes this resistance. In this paper, the N-terminal 110 amino acids of P6 (termed D1) were identified as the resistance-breaking region. D1 also bound full-length P6. Furthermore, binding of W260 D1 to P6 induced higher beta-galactosidase activity and better leucine-independent growth in the yeast two-hybrid system than its CM1841 counterpart. Thus, W260 may evade Tsu-0 resistance by mediating P6 self-association in a manner different from that of CM1841. Because Tsu-0 resistance prevents virus movement, interaction of P6 with P1 (CaMV movement protein) was investigated. Both yeast two-hybrid analyses and maltose-binding protein pull-down experiments show that P6 interacts with P1. Although neither half of P1 interacts with P6, the N-terminus of P6 binds P1. Interestingly, D1 by itself does not interact with P1, indicating that different portions of the P6 N-terminus are involved in different activities. The P1-P6 interactions suggest a role for P6 in virus transport, possibly by regulating P1 tubule formation or the assembly of movement complexes.