Discipline: Technology and Engineering
Subcategory: Plant Research
Pranav Maddula - Washington University in St.Louis
Co-Author(s): Debarati Basu, Washington University in St. Louis ; Elizabeth S. Haswell, Washington University in St. Louis
The MscS‐Like (MSL) family of proteins contains 10 mechanosensitive (MS) ion channels in Arabidopsis. The functions of these proteins range from maintaining redox homeostasis in mitochondria to cellular signaling and cell death. One member, MSL10, has two separate functions, conducting ions in response to membrane tension and signaling for cell death. The N-terminus alone can promote cell death. At least 9 amino acids in the N-terminus are phosphorylated, with signaling cascades being activated when they are dephosphorylated. We were interested in identifying single nucleotide polymorphisms (SNPs) in MSL10 using genomes from the 1001 genomes project, a repository for whole-genome sequence variation data in 1135 strains of Arabidopsis thaliana. These strains are collected from around the world, and as such are products of natural selection under diverse ecological conditions. We extracted the sequences for the MSL family in the 1135 lines and analyzed each in reference to Arabidopsis thaliana Columbia-0. We then focused our analysis on non-synonymous substitutions, a type of SNP that alters the amino acid sequence. We noticed fewer non-synonymous SNPs in the MscS homology domain of MSL10 than in the N-terminus or C-terminus. No SNPs were found at any of the phosphorylated sites, which are known to be important for MSL10’s signaling function. Furthermore, there are SNPs in a majority of the analyzed Arabidopsis accessions, indicating that MSL10 is somewhat tolerant to amino acid sequence changes. Another protein of interest is PIEZO—a plant homolog to the PIEZO family of MS ion channels found in animals. In animals, PIEZO plays a role in processes from touch sensation to neuron development. In AtPIEZO, we saw a similar number of SNPs when compared to MSLs, which may indicate that AtPIEZO has a greater evolutionary pressure preventing mutations, indicating a yet to be found function. These results form the foundation for future analysis of geographic divergence of Arabidopsis lines and the mutations present in those lines.
Funder Acknowledgement(s): NSF/CEMB awarded to E. Haswell
Faculty Advisor: Elizabeth Haswell, firstname.lastname@example.org
Role: The entire project was completed by me. This project is the culmination of an entire summer's worth of work from an NSF REU. Everything from the initial data mining and data processing to the analysis of genetic variations and phylogenies was completed by me.