It was only 30 years ago that scientists discovered that some micoorganisms constituted a new "Domain" of life, the Archaea. Today we know that they represent as much as one third of the diversity of life on Earth. These microbes appear indistinguishable from bacteria under the microscope, but at the molecular level they are actually more closely related to plants and animals. Diverse archaeal species are notable for being able to thrive in extremes of temperature (boiling hot springs, within Antarctic ice), high pressure, acidic pH, or Dead Sea-like high salt conditions. Other archaea inhabit the soil, human and animal digestive tracts, and all depths of the ocean. In spite of their major contributions to our biosphere, we currently have very little understanding of how their genes are used and regulated. High throughput sequencing of microbes has focused almost exclusively on decoding genomic DNA, the genetic instructions for life. However, sequencing a related genetic material from cells, RNA, gives a rich source of information for when genes are used, and how they might be regulated. This approach has revolutionized our understanding of biology through the discovery of "microRNAs" and "RNA interference" and how they control all aspects of cell function. This project seeks to apply the latest new gene sequencing technology to discover thousands of unknown RNA genes across a broad sampling of 24 key species of Archaea. The new data will also enable creation of new probabilistic models for new RNA gene families, and vastly improve automated RNA gene annotation for newly decoded species.
This project will catalyze many areas of archaeal RNA gene research, including discovery of: novel structural and regulatory RNAs, the mechanism and evolution of Clustered Regularly Interspaced Short Palindrome Repeat (CRISPR) cell immunity, RNA gene processing motifs, and locating genes regulated by RNA "antisense" transcripts. Nearly a dozen collaborating labs will be involved. Graduate students in the lab will be trained in the integration of cutting edge, high-throughput sequencing and bioinformatic approaches to RNA analysis. Collection of new RNA gene data across 24 species, all within the Archaeal Genome Browser comparative framework (developed in the same lab), will stimulate pooling of knowledge, exchange of ideas between groups, and inspire many new research directions in archaeal biology. Ultimately, a better understanding of gene regulation in archaea will enable other groups to study their effect on the biosphere, and potentially engineer useful new properties to address issues as fundamental as global warming and remediation of environmental pollution.
