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Do Nucleotides Flanking miRNA Target Sites Affect Repression Efficacy?
Seth Polydore, Lead Researcher, The Pennsylvania State University
Manipulation of plant physiology is important to bioengineer
crops that are able to adapt to the changing abiotic (higher CO2 levels,
soil salinity, changing climates, etc.) and biotic (pathogenic and parasitic)
stresses. Artificial micro RNAs (a-miRNAs) are one such way to achieve
this. Much research in plants miRNAs has elucidated the complementarity
requirements to maximize repression efficacy. Recently, some studies
have begun to identify factors beyond complementarity that affects the
miRNA repression efficacy – one such factor is the nucleotide context
surrounding the miRNA target site. These factors need to be properly
studied in order to optimize a-miRNA design and targeting algorithms.
Using a dual luciferase assay, we intend to determine how and to what
extent nucleotides flanking an a-miRNA target site are able to impair/
enchance repression efficacy. Our preliminary results show that the changing flanking sequences do indeed seem to change repression; however, underlying biological effects, such as RNA secondary structure and steric hinderances, in relation to these results have yet to be discovered. Overall, our research may reveal provide the first direct evidence linking miRNA repression and oft-ignored factors.
The Spirodela polyrhiza (Giant Duckweed) Expansin Superfamily: A Case of Massive Gene Loss
Nathan Hepler, Graduate Student, Penn State University
Expansins are a superfamily of cell wall-loosening proteins found in plants, which have been implicated in multiple areas of growth and development1,2. Expansins can be divided into four distinct families: alpha-expansin (EXPA), beta-expansin (EXPB), expansin-like A (EXLA) and expansin-like B (EXLB)1. In flowering plants, the expansin superfamily can be further divided into 17 orthologous clades, representing the minimum number of expansin genes in the last common ancestor of monocots and eudicots1. Spirodela polyrhiza is an aquatic monocot, known for its fast doubling time (<30 hours) and potential use as a biofuel and animal feedstock3. Recently, the 158-Mb S. polyrhiza (giant duckweed) genome was sequenced, revealing a severely truncated expansin superfamily (13 members) uncharacteristic of other angiosperms2,3. A total of eight expansin clades are absent in S. polyrhiza, including the EXLB family. Additionally, the remaining expansin genes appear to be undergoing stronger purifying selection, as compared to orthologous sequences in other flowering plants. These results suggest S. polyrhiza may contain the minimum number of expansins necessary for rudimentary plant growth and development.
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