{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/122105"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/122105","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Insight into the effects of conjugative plasmids in the hyperthermophilic archaeon Sulfolobus islandicus: A mechanistic and populational perspective","abstract":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2025-12-01","abstract_html":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2025-12-01","abstract_has_math":false,"creators":["Sanchez-Nieves, Ruben Leonardo"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Microbiology","degree_department":null,"school":null,"contributors":["Whitaker, Rachel","Metcalf, William","Kuzminov, Andrei","Cann, Isaac"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2023,"date_issued":"2023-12","date_published":"2023-12","updated_at":"2026-07-22T22:25:00Z","subjects":["Sulfolobus","Plasmids","Recombination","Gene Transfer"],"languages":["en","eng"],"rights":["Copyright 2023 Ruben Sanchez-Nieves"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/122105","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Whitaker, Rachel","Metcalf, William","Kuzminov, Andrei","Cann, Isaac"]},{"key":"dc:creator","label":"Author","values":["Sanchez-Nieves, Ruben Leonardo"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2023-12","2023-11-14"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Microbiology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Sulfolobus","Plasmids","Recombination","Gene Transfer"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2023 Ruben Sanchez-Nieves"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/122105"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2025-12-01","The student, Ruben Sanchez-Nieves, accepted the attached license on 2023-11-09 at 07:38.","The student, Ruben Sanchez-Nieves, submitted this Dissertation for approval on 2023-11-09 at 07:52.","This Dissertation was approved for publication on 2023-11-14 at 16:02.","DSpace SAF Submission Ingestion Package generated from Vireo submission #19898 on 2024-03-01 at 13:29:34","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."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Insight into the effects of conjugative plasmids in the hyperthermophilic archaeon Sulfolobus islandicus: A mechanistic and populational perspective"]}]}],"canonical_facts":{"dc:contributor":["Whitaker, Rachel","Metcalf, William","Kuzminov, Andrei","Cann, Isaac"],"dc:creator":["Sanchez-Nieves, Ruben Leonardo"],"dc:date":["2023-12","2023-11-14"],"dc:description":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2025-12-01","The student, Ruben Sanchez-Nieves, accepted the attached license on 2023-11-09 at 07:38.","The student, Ruben Sanchez-Nieves, submitted this Dissertation for approval on 2023-11-09 at 07:52.","This Dissertation was approved for publication on 2023-11-14 at 16:02.","DSpace SAF Submission Ingestion Package generated from Vireo submission #19898 on 2024-03-01 at 13:29:34","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."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/122105"],"dc:language":["en","eng"],"dc:rights":["Copyright 2023 Ruben Sanchez-Nieves"],"dc:subject":["Sulfolobus","Plasmids","Recombination","Gene Transfer"],"dc:title":["Insight into the effects of conjugative plasmids in the hyperthermophilic archaeon Sulfolobus islandicus: A mechanistic and populational perspective"],"dc:type":["text"],"thesis:degree_discipline":["Microbiology"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:00Z"}