I am interested in understanding the process of transcription, in which the information encoded by DNA is converted to functional or message containing RNA. I have a particular interest in eukaryotic-type transcription systems, which are found in eukaryotes and also in a little-known but ubiquitous and diverse group of unicellular, anucleate organisms called the archaea.
The archaea physically resemble bacteria--they are small, they lack a nuclear membrane--but these organisms are evolutionarily distinct from bacteria, just as bacteria are distinct from eukaryotes. In short, the archaea make up a third form of life, in addition to bacteria and eukaryotes. At the level of their molecular biology (transcription, translation, and DNA replication), the archaea are more closely related to eukaryotes than to bacteria, suggesting that archaea and eukaryotes have a shared ancestry that diverged from the bacterial lineage early in evolution.
The archaea present a wonderful opportunity for studying the basic mechanisms of eukaryotic-type transcription systems, in that few components are apparently required for accurate transcription initiation, in contrast to the large number of transcription factors that are required for eukaryotic transcription. Specific, promoter-dependent transcription initiation can ve reconstituted in vitro with the following archaeal components: promoter DNA, two transcription factors (TBP and TFB) and RNA polymerase.
In my postdoctoral work, I used DNA-protein cross-linking techniques to analyze a biochemically purified transcription system from the hyperthermophilic aarchaean Pyrococcus furiosus. Results from these studies indicate the positions of TBP, TFB, and RNA polymerase subunites relative to DNA in the archaeal transcription initiation complex, and suggest possible roles for TBP and TFB in the process of initiation. Theses studies have provided a framework for in depth analysis of the archaeal transcription mechanism.
The research in my lab is directed at the following questions:
1) How do the transcription factors and RNA polymerase interact to form the transcription initiation complex? Do these interactions change during the process of initiation? What are the protein and DNA determinants for transcription complex assembly, and how does DNA sequence define the efficiency of transcription initiation? 2) How does the transcription machinery interact with other cellular components--which proteins encoded by the archaeal genome interact with and regulate the function of the transcription factors and RNA polymerase? 3) As a longer-term goal, how is archaeal transcription regulated during cell growth and response to environmental stimuli?
We are using the hyperthermophile Pyrococcus furiosus as a model organism, applying the techniques of biochemistry, molecular biology, and bioinformatics to investigate these questions. A better understanding of the basic mechanisms of archaeal transcription should help in understanding eukaryotic transcription and the evolution of the eukaryotic-type transcription mechanism. In addition these studies will contribute to a growing body of research aimed at understanding the basic biology of the archaea.