Molecular Evolution

Evolution of stress tolerance in the genus Boechera:
Boechera is a large genus of North American plants in the Brassicaceae family. We are studying the evolution of stress responses in the California Boechera. We are interested in understanding how plants response to stress and how stress responses evolve in natural populations. We have collections of Boechera seeds from natural populations across California. We are examining and monitoring Boechera response to high heat, light and oxidative stress.

Related Publications and Presentations

Between a rock cress and a hot place: multiple abiotic stresses in plants Genna C. Gallas*, Sarah D’Antonio*, Elizabeth Waters*, Plant Biology Meeting July 2014 Portland OR.

Comparative Transcriptomics of Thermotolerance in Arabidopsis and Boechera. Abdulla Jamalli*, Genna Gallas* and Elizabeth Waters. International Plant and Animal Genome Conference 2014 San Diego, CA

Gene, Protein and Genome Evolution:
My lab conducts research on how gene and genome evolve. Topics of past and current research interest include the, genome evolution and annotation origin and evolutionary history of pseudogenes. I am interested in how gene expression influences evolutionary rate and with colleagues at U. C. Irvine we have examined the evolutionary dynamics of “lowly expressed” genes. We have found that these genes may represent a transition from functional to pseudogenes.

Related Publications and Presentations

Yang, L., Takuno, S., Waters, E. R., Gaut, B.S. 2011 Lowly expressed genes in Arabidopsis thaliana bear the signature of possible pseudogenization by promoter degredation. Mol. Biol. Evol. 28: 1193-1203.

Waters, E.R., Nguyen S*, Eskandar, R*, Behan, J* and Sanders-Reed S.* 2008 The recent evolution of a pseudogene: diversity and divergence of a mitochondrial-localized small heat shock protein in Arabidopsis thaliana. Genome 51:177-86.

I am interested in how evolutionary analysis can inform structure function studies and have collaborated with biochemists and molecular biologists on studies of heat shock proteins, Fibroblast Growth Factor proteins and TMEM proteins.

Lee JH, Silhavy JL, Lee JE, Al-Gazali L, Thomas S, Davis EE, Bielas SL, Hill KJ, Iannicelli M, Brancati F, Gabriel SB, Russ C, Logan CV, Sharif SM, Bennett CP, Abe M, Hildebrandt F, Diplas BH, Attie-Bitach T, Katsanis N, Rajab A, Koul R, Sztriha L, Waters ER, Ferro-Novick S, Woods CG, Johnson CA, Valente EM, Zaki MS, Gleeson JG (2012) Evolutionarily assembled cis-regulatory module at a human ciliopathy locus. Science 335: 966-969

Basha, E., Jones, C., Blackwell, A. E. Cheng, G. Waters, E. R. Samsel, K. A. Siddique, M. Pett, V. Wysocki, V. Vierling, E. 2013. An unusual dimeric small heat shock protein provides insight into the mechanism of this class of chaperones Journal of Molecular Biology 425: 1683-96.

Lee U., Rioflorido I. *, Hong S.W., Larkindale J., Waters E., Vierling E. 2007 The Arabidopsis ClpB/Hsp100 family of proteins: Chaperones for stress and chloroplast development. The Plant Journal 49:115-127.

Evolution of the Heat Shock Proteins:
I have long been interested evolution of the heat shock response and the heat shock proteins. My students and I have traced the origin of the diverse small heat shock proteins in the green plant lineage, from green algae to angiosperms. We have found that the mitochondrial and chloroplast sHSPs did not originate from bacterial endosymbionts but rather from nuclear-encoded cytosolic proteins. I am also interested in the selective pressures acting on heat shock proteins within and across closely related species. My student Jim Starrett and I have found evidence of positive selection acting on HSP70s in spiders.

Related Publications and Presentations

Waters, E. R. 2014 Conservative Innovation: the mixed up evolutionary history of the heat shock proteins. The Biochemist. 36:9-22
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Waters, E. R. 2013 Darwin Review: The evolution, function, structure, and expression of the plant sHSPs. Journal of Experimental Botany. 64: 391-403.
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Aevermann B.D*. and Waters E.R. 2008 The duplication and retention of the small heat shock protein gene family in Caenorhabditis elegans and Caenorhabditis briggsae. 133:307-319. Genetica.
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Waters E.R., Aevermann, B.D.*, Sanders-Reed, Z.* 2008 Comparative analysis of the small heat shock proteins in three angiosperm genomes identifies new subfamilies and reveals diverse evolutionary patterns. 13:127-142. Cell Stress & Chaperones
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Starrett J.* and Waters E.R. 2007 Positive natural selection has driven the evolution of the Hsp70s in Diguetia spiders. Biology Letters 3:439-444.
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Origin of Land Plants:
The origin of land plants was one of the major evolutionary transitions in the history of life. I have been interested in the molecular adaptations that were associated with the transition from life in the water to the terrestrial habitat, and in particular the impact this had on the diversity and evolution of the heat shock proteins.

Related Publications and Presentations

Rensing et al. 2008 The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science. 2008 319(5859): 64-9.
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Waters, E.R. Molecular Adaptation and The Origin of Land Plants. 2003 Molecular Phylogenetics and Evolution. 29: 456-463.
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Waters E.R and Rioflorido I.* 2007 Evolutionary analysis of the small heat shock proteins in five complete algal genomes. Journal of Molecular Evolution. 65:162-174
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Renner, T.* and Waters E.R. 2007 Comparative genomic analysis of the HSP70s in five diverse algal species. Cell Stress & Chaperones. 12:172-185.
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Recent Collaborators:

Brandon Gaut, UC Irvine.
Joseph Gleeson UC San Diego
Jaakko Kanjcvki U. of Helsinki
Elizabeth Vierling University of Massachusettes Amherst