Gene Expression in Archaea: Studies of Transcriptional Promoters, Messenger RNA Processing, and Five Prime Untranslated Regions in Methanocaldococcus Jannashchii
Zhang, Jian
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https://hdl.handle.net/2142/72519
Description
Title
Gene Expression in Archaea: Studies of Transcriptional Promoters, Messenger RNA Processing, and Five Prime Untranslated Regions in Methanocaldococcus Jannashchii
Author(s)
Zhang, Jian
Issue Date
2009
Doctoral Committee Chair(s)
Olsen, Gary J.
Department of Study
Microbiology
Discipline
Microbiology
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Biology, Microbiology
Abstract
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.
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