Identifying conserved alternative splicing (AS) events among evolutionarily distant species can prioritize AS events for functional characterization and help uncover relevant cis-and trans-regulatory factors. A genome-wide search for conserved cassette exon AS events in higher plants revealed the exonization of 5S ribosomal RNA (5S rRNA) within the gene of its own transcription regulator, TFIIIA (transcription factor for polymerase III A). The 5S rRNA-derived exon in TFIIIA gene exists in all representative land plant species but not in green algae and nonplant species, suggesting it is specific to land plants. TFIIIA is essential for RNA polymerase III-based transcription of 5S rRNA in eukaryotes. Integrating comparative genomics and molecular biology revealed that the conserved cassette exon derived from 5S rRNA is coupled with nonsense-mediated mRNA decay. Utilizing multiple independent Arabidopsis overexpressing TFIIIA transgenic lines under osmotic and salt stress, strong accordance between phenotypic and molecular evidence reveals the biological relevance of AS of the exonized 5S rRNA in quantitative autoregulation of TFIIIA homeostasis. Most significantly, this study provides the first evidence of ancient exaptation of 5S rRNA in plants, suggesting a novel gene regulation model mediated by the AS of an anciently exonized noncoding element.
MicroRNAs (miRNA) are small regulatory, noncoding RNA molecules that are transcribed
as primary miRNAs (pri-miRNA) from eukaryotic genomes. At least in plants, their
regulatory activity is mediated through base-pairing with protein-coding messenger RNAs
(mRNA) followed by mRNA degradation or translation repression.
We describe NOVOMIR, a program for the identification of miRNA genes in plant
genomes. It uses a series of filter steps and a statistical model to discriminate a pre-miRNA
from other RNAs and does rely neither on prior knowledge of a miRNA target nor on
comparative genomics. The sensitivity and specificity of NOVOMIR for detection of premiRNAs
from Arabidopsis thaliana is ~0.83 and ~0.99, respectively. Plant pre-miRNAs
are more heterogeneous with respect to size and structure than animal pre-miRNAs. Despite
these difficulties, NOVOMIR is well suited to perform searches for pre-miRNAs on a
genomic scale. NOVOMIR is written in Perl and relies on two additional, free programs for prediction
of RNA secondary structure (RNALFOLD, RNASHAPES).
The RNase P RNA (rnpB) and protein (rnpA) genes were identified in the two Aquificales Sulfurihydrogenibium azorense and Persephonella marina. In contrast, neither of the two genes has been found in the sequenced genome of their close relative, Aquifex aeolicus. As in most bacteria, the rnpA genes of S. azorense and P. marina are preceded by the rpmH gene coding for ribosomal protein L34. This genetic region, including several genes up-and downstream of rpmH, is uniquely conserved among all three Aquificales strains, except that rnpA is missing in A. aeolicus. The RNase P RNAs (P RNAs) of S. azorense and P. marina are active catalysts that can be activated by heterologous bacterial P proteins at low salt. Although the two P RNAs lack helix P18 and thus one of the three major interdomain tertiary contacts, they are more thermostable than Escherichia coli P RNA and require higher temperatures for proper folding. Related to their thermostability, both RNAs include a subset of structural idiosyncrasies in their S domains, which were recently demonstrated to determine the folding properties of the thermostable S domain of Thermus thermophilus P RNA. Unlike 16S rRNA phylogeny that has placed the Aquificales as the deepest lineage of the bacterial phylogenetic tree, RNase P RNA-based phylogeny groups S. azorense and P. marina with the green sulfur, cyanobacterial, and d/e proteobacterial branches.
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