Gene expression in Archaea is less understood than those in Bacteria and Eucarya. In general, three steps are involved in gene expression--transcription, RNA processing, and translation. To expand our knowledge of these processes in Archaea, I have studied transcriptional promoters, messenger RNA processing, and 5'-untranslated regions in "Methanocaldococcus (Methanococcus) jannaschii". The promoters in "M. jannaschii" are similar to eukaryotic RNA polymerase II promoters, with a TATA box and a transcription factor B recognition element being the core promoter elements. Protein-coding gene promoters bind transcription factors less tightly than do most tRNA gene promoters. Results show a correlation between promoter sequence and transcription factor binding affinity. Much of gene expression in "M. jannaschii" may be determined by intrinsic promoter strength. Messenger RNA processing is common in "M. jannaschii". RNA cleavage occurs in the upstream regions of 20% of the protein-coding genes examined. The cleavage is endonucleolytic. Most cleavage sites are located 12-16 nucleotides upstream of the corresponding translation start site, suggesting that the processing may be associated with translation. The processing alters the representation of various genes in the RNA pool, and therefore may play a significant role in defining the balance of proteins in the cell. Systematic investigation of the occurrences and characteristics of ribosome binding sites, RNA secondary structures, and upstream AUGs and open reading frames in the 5'-untranslated regions of mRNAs in "M. jannaschii" reveals that the ribosome binding site is important for protein translation while the other features do not commonly play roles in gene expression. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]