Epigenetic inheritance in the Crenarchaeota

University Of Nebraska-Lincoln, Lincoln NE

Investigators

Abstract

This project addresses evolution by studying how microbes called archaea inherit biological traits through an epigenetic mechanism. Epigenetics refers to chemical modifications of DNA or of proteins bound to that DNA that cause inherited changes without modifying the order of nucleotides (sequence) of a gene. This form of heredity has significant impacts on the physiology and evolution of animals and plants but it is not known when this form of inheritance arose in evolution. This project explores the possibility that epigenetic inheritance arose first in in the archaea, which are a much more ancient lineage than eukaryotes including plants and animals. The PI will examine laboratory-adapted lineages of an archaeal species that inherit extreme resistance to acidic environments. These cells have extensive changes in gene expression that enable this acid resistance, yet they do not have any DNA sequence variations that explain this inherited trait. This project will also enable development a new investigative laboratory course module for a general microbiology course (400 students/year). The laboratory module will be adapted for use in high schools and with underserved minority students (in the U.S Department of Education Upward Bound program) and in a regional Women in Science program. SARC archaeal lines were evolved in the laboratory to select for extreme acid resistance. In some of the SARC lines, chromatin protein hypomethylation and not mutation account for inherited global changes in gene expression that are responsible for extreme acid resistance. In the proposed work, the locus-specific distribution of epigenetic marks on chromatin proteins will be determined using called site-specific chromatin immunoprecipitation-mass spectrometry. These experiments will determine whether hypomethylated archaeal chromatin proteins preferentially localize to genes within the SARC transcriptome. While the composition and epigenetic variation of chromatin protein networks have been established, the connectivity among component proteins has not. These networks are critical because they may constitute the signal transduction pathway controlling epigenetic traits. The PI will use three different techniques to elucidate how the proteins are connected in one or more networks. Finally, the PI will investigate the observation that SARC lines have a reduced mutation rate per cell division. The PI will test two competing models to clarify the mechanism underlying this trait. This work has the potential to reveal that epigenetic inheritance is an ancient mechanism for adaptation to sudden environmental changes typified by steep physiochemical gradients. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.