{"id":{"repo_id":"iu","oai_identifier":"oai:scholarworks.iu.edu:2022/19579"},"canonical_url":"https://search.dev.ndltd.org/etd/iu/oai:scholarworks.iu.edu:2022/19579","repository":{"repo_id":"iu","name":"Indiana University","base_url":"https://scholarworks.iu.edu/iuswrrest/oai/request"},"display":{"title":"Light-sensing in bacteria","abstract":"Light reception plays an important role in regulating lifestyle changes in bacteria. My research focused on a number of different light-sensing systems in different bacteria: PpaA in Rhodobacter sphaeroides, PixD-PixE in Synechocystis sp. PCC, and the known light-receptors in Rhodospirillum centenum. PpaA from R. sphaeroides had previously been shown to be a heme-binding protein, despite its sequence similarity to cobalamin-binding proteins. My research showed that PpaA is in fact a bona fide cobalamin-binding protein. PpaA binds specifically hydroxy-cobalamin, but not other forms of cobalamin. PpaA does have some ability to bind heme, but a mutant form of PpaA that showed better heme-binding was inactive in vivo. This suggests that PpaA functional cofactor is cobalamin, rather than heme. We also tested cobalamin-binding in a number of homologs of PpaA and found that almost all are indeed cobalamin-binding proteins. The genome of Rhodospirillum centenum contains four reading frames that encode light sensing proteins. We identified possible role for each of these light-receptors by making deletion mutants, and testing the impact of these deletion on the transcription levels. Our results suggest that the PYP-phytochrome hybrid Ppr plays a role as a global regulator of transcription. A BLUF and a bacteriophytochrome on the other hand showed changes in expression levels of a number of genes involved in motility. Lastly, deletion of a LOV domain containing protein did not result in any significant changes in gene expression levels. This suggests that the LOV protein does not regulate life-style changes, but rather controls immediate responses. PixD is a short BLUF protein that has been shown to play a role in regulating phototaxis in Synechocystis sp. PCC6803. We were able to show that Slr1692, encoded by an ORF upstream of pixE-pixD might play a role in regulating phototaxis.","abstract_html":"Light reception plays an important role in regulating lifestyle changes in bacteria. My research focused on a number of different light-sensing systems in different bacteria: PpaA in Rhodobacter sphaeroides, PixD-PixE in Synechocystis sp. PCC, and the known light-receptors in Rhodospirillum centenum. PpaA from R. sphaeroides had previously been shown to be a heme-binding protein, despite its sequence similarity to cobalamin-binding proteins. My research showed that PpaA is in fact a bona fide cobalamin-binding protein. PpaA binds specifically hydroxy-cobalamin, but not other forms of cobalamin. PpaA does have some ability to bind heme, but a mutant form of PpaA that showed better heme-binding was inactive in vivo. This suggests that PpaA functional cofactor is cobalamin, rather than heme. We also tested cobalamin-binding in a number of homologs of PpaA and found that almost all are indeed cobalamin-binding proteins. The genome of Rhodospirillum centenum contains four reading frames that encode light sensing proteins. We identified possible role for each of these light-receptors by making deletion mutants, and testing the impact of these deletion on the transcription levels. Our results suggest that the PYP-phytochrome hybrid Ppr plays a role as a global regulator of transcription. A BLUF and a bacteriophytochrome on the other hand showed changes in expression levels of a number of genes involved in motility. Lastly, deletion of a LOV domain containing protein did not result in any significant changes in gene expression levels. This suggests that the LOV protein does not regulate life-style changes, but rather controls immediate responses. PixD is a short BLUF protein that has been shown to play a role in regulating phototaxis in Synechocystis sp. PCC6803. We were able to show that Slr1692, encoded by an ORF upstream of pixE-pixD might play a role in regulating phototaxis.","abstract_has_math":false,"creators":["Vermeulen, Albertus Jan"],"institution":"[Bloomington, Ind.] : Indiana University","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Bauer, Carl E"],"committee_chairs":[],"committee_members":[],"year":2015,"date_issued":"2015-02","date_published":"2015-02","updated_at":"2026-07-24T02:40:00Z","subjects":["cobalamin","light receptors","phototaxis","Rhodobacter sphaeroides","Rhodospirillum centenum","Synechocystis sp. PCC6803"],"languages":["en"],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2022/19579","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Bauer, Carl E"]},{"key":"dc:creator","label":"Author","values":["Vermeulen, Albertus Jan"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2015-02-13T08:23:06Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2015-02-13T08:23:06Z"]},{"key":"dc:date.issued","label":"Date","values":["2015-02"]},{"key":"dc:publisher","label":"Institution","values":["[Bloomington, Ind.] : Indiana University"]},{"key":"dc:type","label":"Dc Type","values":["Doctoral Dissertation"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["cobalamin","light receptors","phototaxis","Rhodobacter sphaeroides","Rhodospirillum centenum","Synechocystis sp. 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PpaA from R. sphaeroides had previously been shown to be a heme-binding protein, despite its sequence similarity to cobalamin-binding proteins. My research showed that PpaA is in fact a bona fide cobalamin-binding protein. PpaA binds specifically hydroxy-cobalamin, but not other forms of cobalamin. PpaA does have some ability to bind heme, but a mutant form of PpaA that showed better heme-binding was inactive in vivo. This suggests that PpaA functional cofactor is cobalamin, rather than heme. We also tested cobalamin-binding in a number of homologs of PpaA and found that almost all are indeed cobalamin-binding proteins. The genome of Rhodospirillum centenum contains four reading frames that encode light sensing proteins. We identified possible role for each of these light-receptors by making deletion mutants, and testing the impact of these deletion on the transcription levels. Our results suggest that the PYP-phytochrome hybrid Ppr plays a role as a global regulator of transcription. A BLUF and a bacteriophytochrome on the other hand showed changes in expression levels of a number of genes involved in motility. Lastly, deletion of a LOV domain containing protein did not result in any significant changes in gene expression levels. This suggests that the LOV protein does not regulate life-style changes, but rather controls immediate responses. PixD is a short BLUF protein that has been shown to play a role in regulating phototaxis in Synechocystis sp. PCC6803. We were able to show that Slr1692, encoded by an ORF upstream of pixE-pixD might play a role in regulating phototaxis."]},{"key":"dc:title","label":"Title","values":["Light-sensing in bacteria"]}]}],"canonical_facts":{"dc:contributor.advisor":["Bauer, Carl E"],"dc:creator":["Vermeulen, Albertus Jan"],"dc:date.accessioned":["2015-02-13T08:23:06Z"],"dc:date.available":["2015-02-13T08:23:06Z"],"dc:date.issued":["2015-02"],"dc:description":["Thesis (Ph.D.) - Indiana University, Biochemistry and Molecular Biology, 2015"],"dc:description.abstract":["Light reception plays an important role in regulating lifestyle changes in bacteria. My research focused on a number of different light-sensing systems in different bacteria: PpaA in Rhodobacter sphaeroides, PixD-PixE in Synechocystis sp. PCC, and the known light-receptors in Rhodospirillum centenum. PpaA from R. sphaeroides had previously been shown to be a heme-binding protein, despite its sequence similarity to cobalamin-binding proteins. My research showed that PpaA is in fact a bona fide cobalamin-binding protein. PpaA binds specifically hydroxy-cobalamin, but not other forms of cobalamin. PpaA does have some ability to bind heme, but a mutant form of PpaA that showed better heme-binding was inactive in vivo. This suggests that PpaA functional cofactor is cobalamin, rather than heme. We also tested cobalamin-binding in a number of homologs of PpaA and found that almost all are indeed cobalamin-binding proteins. The genome of Rhodospirillum centenum contains four reading frames that encode light sensing proteins. We identified possible role for each of these light-receptors by making deletion mutants, and testing the impact of these deletion on the transcription levels. Our results suggest that the PYP-phytochrome hybrid Ppr plays a role as a global regulator of transcription. A BLUF and a bacteriophytochrome on the other hand showed changes in expression levels of a number of genes involved in motility. Lastly, deletion of a LOV domain containing protein did not result in any significant changes in gene expression levels. This suggests that the LOV protein does not regulate life-style changes, but rather controls immediate responses. PixD is a short BLUF protein that has been shown to play a role in regulating phototaxis in Synechocystis sp. PCC6803. We were able to show that Slr1692, encoded by an ORF upstream of pixE-pixD might play a role in regulating phototaxis."],"dc:identifier.uri":["https://hdl.handle.net/2022/19579"],"dc:language.iso":["en"],"dc:publisher":["[Bloomington, Ind.] : Indiana University"],"dc:subject":["cobalamin","light receptors","phototaxis","Rhodobacter sphaeroides","Rhodospirillum centenum","Synechocystis sp. PCC6803"],"dc:title":["Light-sensing in bacteria"],"dc:type":["Doctoral Dissertation"]},"updated_at":"2026-07-24T02:40:00Z"}