Insight into the effects of conjugative plasmids in the hyperthermophilic archaeon Sulfolobus islandicus: A mechanistic and populational perspective

Sanchez-Nieves, Ruben Leonardo

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https://hdl.handle.net/2142/122105 Copy

Description

Title

Insight into the effects of conjugative plasmids in the hyperthermophilic archaeon Sulfolobus islandicus: A mechanistic and populational perspective

Author(s)

Sanchez-Nieves, Ruben Leonardo

Issue Date

2023-11-14

Director of Research (if dissertation) or Advisor (if thesis)

Whitaker, Rachel

Doctoral Committee Chair(s)

Whitaker, Rachel

Committee Member(s)

• Metcalf, William
• Kuzminov, Andrei
• Cann, Isaac

Department of Study

Microbiology

Discipline

Microbiology

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• Sulfolobus
• plasmids
• recombination
• gene transfer

Abstract

Horizontal gene transfer has significant repercussions for microbial populations as it allows a break from vertical descent, through which gene diversity is increased and, in some cases, new niches are filled. Canonically, gene transfer occurs through one of three mechanisms: conjugation, transduction, and transformation. However, some organisms, such as Sulfolobus, possess a host encoded system which exchanges DNA within a closely related population. Named the Ced system, this mechanism of gene transfer is activated through DNA damage but is constitutively expressed under normal growth conditions. Simultaneously, Sulfolobus spp. are unique in their possession of conjugative plasmids within the archaeal domain. The work presented in this thesis focuses on plasmid conjugation and plasmids in a populational setting. In Chapter 2, we discuss the effects of possessing an active and integrated conjugative plasmid within the natural gene transfer context in S. islandicus. We find that integration into the chromosome leads to higher recombination frequencies in the surrounding chromosomal regions. Furthermore, we find that TraG performs a key role in conjugation. Differing recombination frequencies across the chromosome have an impact on genome plasticity and the overall evolution of populations. Chapter 3 takes a different perspective on conjugative plasmids in Sulfolobus. In this chapter, we investigate S. islandicus natural isolates from the Nymph Lake region of Yellowstone National Park. We utilize PacBio HiFi sequencing on a subset of isolates in order to serve as references for the population. `We find that there are two major groups found within Nymph Lake. Additionally, we find that conjugative plasmids are widespread throughout the population. We then take a closer look at the plasmids and find evidence of CRISPR targeting and subsequent recombination between plasmid types. In Chapter 4, we discuss the comparative transcriptomic portion of a broader study focusing on S-layer function in S. islandicus M.16.4. We compared the expression patterns of cells in exponential and stationary in each of the mutants surveyed. We found that gene expression changes are substantially less drastic in an S-layer deficient culture. We hypothesize that the absence of the S-layer is leading to a stress response that exacerbates the aggregation phenotype present in all S. islandicus strains. This may lead to nutrient depletion in these cells, additionally the absence of the S-layer would also remove the periplasmic space potential of vital importance to cell metabolism.

Graduation Semester

2023-12

Type of Resource

Thesis

Copyright and License Information

Copyright 2023 Ruben Sanchez-Nieves

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