Non-Coding Genomics of Methanocaldococcus Jannaschii: A Survey of Promoters, Non-Coding RNA Genes, and Repetitive DNA Elements

Non-protein-coding sequences of a genome carry out various tasks which contribute to the functionality of the genome as an information carrier. They are essential genomic components and are operative in genetic information remission, transfer, and processing---key processes where the three domains of life, Bacteria, Archaea, and Eucarya, differ from one another. This thesis focuses on some non-coding features of an archaeal genome, that of Methanocaldococcus jannaschii, in an effort to identify and characterize promoters, non-coding RNA genes, and novel repetitive DNA sequences. Genome-wide identification of transcription factor binding sites revealed archaeal core promoter elements, which include TATA box, BRE, and an initiator element. The structural similarity between archaeal basal promoters and those from Eucarya has reinforced the relationship between them. A quantification of transfer RNA (tRNA) abundance showed a correlation between codon usage frequency and the intracellular cognate tRNA concentration in this organism. Further characterization of tRNA gene promoters indicated that a key determinant of tRNA expression levels is the differential affinity of transcription factors to various tRNA gene promoters. The whole genome approach of promoter searching also led to the identification of several non-coding RNA genes. Nonprotein-coding RNA (ncRNA) promoters share the same set of core elements but with more deviations from the consensus compared to those of tRNA genes; in accordance, they possess lower affinity to the transcription factors. Some additional ncRNA transcripts were isolated in M. jannaschii; they are located in intergenic or intragenic regions, and encoded sense or antisense relative to the surrounding or enclosing genes. These novel transcripts further confirm the high abundance and diversity of ncRNA genes in this genome. Lastly, groups of novel repetitive DNA elements (nontandem short repeat, NTSR) were identified in M. jannaschii, by a search strategy which combines sequence and secondary structure information. These NTSRs share essential characters similar to bacterial REPs, in terms of the abundance, G+C content, structure, and genome-wide location.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biochemistry

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2015

Author dc:creator

• Li, Enhu

Contributors dc:contributor

• Gary Olsen

• Biology, Molecular

Language dc:language

eng

Identifier

(MiAaPQ)AAI3301180

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/84848