Conservation & Comparative Genomics of Archaea: Novel, Lineage Specific Adaptations in Transcription Machinery

Author

• Suzie Lorraine Drew, Portland State UniversityFollow

Sponsor

Portland State University. Department of Biology

First Advisor

Michael Bartlett

Term of Graduation

Summer 2026

Date of Publication

8-19-2026

Document Type

Dissertation

Degree Name

Doctor of Philosophy (Ph.D.) in Biology

Department

Biology

Language

English

Subjects

Archaea, Comparative genomics, RNA polymerase, Transcription

Physical Description

1 online resource (xii, 141 pages)

Abstract

This research investigated the conservation of transcription factor E alpha (TFE-α) across the entirety of the archaeal domain. TFE-α is a near-ubiquitous, general transcription factor within Archaea with homology to eukaryotic TFIIE-α, and is characterized as essential for archaeal transcription in vivo. It was previously reported that two members of the Thermoplasma genus lack TFE-α. Known TFE-α sequences were used to identify TFE-α sequences across the entire archaeal domain using BLASTP and multiple annotation sources. This research confirms previous observations of TFE-α absence within the entire Thermoplasma genus, and further shows that TFE-α is present in just 1.12% of the 4,028 Thermoplasmatota phylum genomes examined. Additionally, multiple DPANN super-phylum lineages lack a TFE-α gene. The Aenigmatarchaeota, EX4484-52, Nanohalarchaeota, and Huberarchaeota had zero detected TFE-α sequences and the Micrarchaeota had unexpectedly low frequency of TFE-α genes (25.58%). The Panguiarchaeaceae family of the Asgardarchaeota was also observed to completely lack TFE-α genes. Alignment of identified TFE-α sequences from across the archaeal domain reveals highly conserved extended winged-helix, leucine zipper, and zinc ribbon motifs as expected for this protein. Partial, lineage-specific presence of TFE-α within the Thermoplasmatota and Micrarchaeota phyla did not reveal highly divergent TFE-α sequences nor could these samples be used to recover more TFE-α sequences from the rest of the phylum. All Archaeal genomes observed to lack TFE-α are from co-cultured or proposed symbionts, with the exception of members of the Thermoplasmatota phylum. Analysis of known archaeal hosts-ymbiont pairings revealed that in each case, one member of the pair did not have TFE-α detected while the other member did. While symbionts may obtain TFE-α function for transcription through host supplementation, our current understanding of archaeal transcription initiation mechanism cannot account for the absence of TFE-α within the free-living Thermoplasmatota phylum. This suggests the presence of alterative factors or an alternative mechanism that confers function similar to that of TFE-α in Thermoplasmatota. Research into the structural diversity of the RNA polymerase and general transcription factors within the Thermoplasmatota may help determine how transcription initiation may function without this essential protein.

Rights

© 2026 Suzie Lorraine Drew

Comments

Funded in part by US-National Science Foundation grant DEB-2409507 awarded to A.L. Reysenbach, a Portland State University faculty enhancement award to M. Bartlett, and a Forbes Forbes Lea Fund award to S. Drew.

Recommended Citation

Drew, Suzie Lorraine, "Conservation & Comparative Genomics of Archaea: Novel, Lineage Specific Adaptations in Transcription Machinery" (2026). Dissertations and Theses. Paper 7228.