The basal transcription complex of Archaea resembles that of Eukarya whilst at the same time utilizing classical bacterial transcription regulators. The regulation of tryptophan biosynthesis has served as a model system for many organisms and was therefore an obvious choice for the initial studies of regulation in M. thermautotrophicus.  The M. thermautotrophicus tryptophan-responsive transcription regulator, TrpY, regulates its own expression as well as that of the divergently transcribed tryptophan biosynthesis operon. Additionally TrpY regulates expression of the trpB2 gene that encodes for a homolog of the tryptophan beta-synthase located elsewhere on the genome.  Repression of the trpB2 gene is achieved through a two-step mechanism whereby TrpY binds in a sequence specific manner followed by a nucleation event.   The nucleation event then blocks access of the basal transcription factors to the promoter.  The regulation of tryptophan biosynthesis has laid the ground work for understanding transcription regulation in M. thermautotrophicus and further study of transcriptional regulation of the methanogenesis pathway and cellular stress responses will prove useful in understanding the full potential of methanogens in industrial systems.