{"id":{"repo_id":"ghent","oai_identifier":"oai:archive.ugent.be:469245"},"canonical_url":"https://search.dev.ndltd.org/etd/ghent/oai:archive.ugent.be:469245","repository":{"repo_id":"ghent","name":"Ghent University","base_url":"https://biblio.ugent.be/oai"},"display":{"title":"Towards unveiling the Photoactive Yellow Proteins: characterization of a halophilic member and a proteomic approach to study light responses","abstract":"The family of blue-light absorbing Photoactive Yellow Proteins (PYPs) has become an attractive model system to study the molecular events related to light perception. PYP covalently binds a p-hydroxycinnamic acid chromophore, which is fine-tuned for efficient light absorption and initiates a photocycle by a trans to cis isomerization. PYPs were originally discovered in a number of halophilic proteobacteria, but the pyp gene distribution actually spans a wider spectrum of both phototrophic as well as non-photosynthetic bacteria. PYP from Salinibacter ruber is shown to be the first example of a truly halophilic PYP that is stabilized by ionic strength. Furthermore, illumination with blue light ignites a cyclic series of dark reactions including the typical intermediates I1, I2 and I2’, which suggests that it is functional although the recovery to the dark-adapted state was observed to be the slowest of any PYP. More interestingly, PYP from Salinibacter ruber contains an unusual 31-residue N-terminal extension which appears to be disordered relative to the remainder of the protein and which induces a unique dimerization of the photosensor with no precedents described before with any of the other published PYPs. Truncation of the N-terminal extension does not seem to influence the photochemical properties, and no structural motif or functional relevance towards signaling could thus far be established. PYP can also be part of multi-domain proteins such as Ppr from the phototroph Rhodospirillum centenum, where it forms the N-terminal domain that is followed by a central bacteriophytochrome (Bph) domain and by a C-terminal histidine kinase domain. The PYP domain acts as a blue-light switch reversing the effects of red light on the Bph domain, resulting in a light-regulated histidine kinase activity of Ppr. Comparative proteomics of wild-type Rh. centenum relative to a ppr gene deletion mutant revealed complex alterations in response to actinic blue- (390 - 510 nm) and red- (>600 nm) light conditions during photosynthetic growth. Differentially regulated proteins provide indications that the Ppr-mediated photoresponse involves an increased acetyl-CoA pool causing a shift in the lipid metabolism in favor of polyketide biosynthesis. However, the nature of this adaptation remains unclear and requires further study.","abstract_html":"The family of blue-light absorbing Photoactive Yellow Proteins (PYPs) has become an attractive model system to study the molecular events related to light perception. PYP covalently binds a p-hydroxycinnamic acid chromophore, which is fine-tuned for efficient light absorption and initiates a photocycle by a trans to cis isomerization. PYPs were originally discovered in a number of halophilic proteobacteria, but the pyp gene distribution actually spans a wider spectrum of both phototrophic as well as non-photosynthetic bacteria. PYP from Salinibacter ruber is shown to be the first example of a truly halophilic PYP that is stabilized by ionic strength. Furthermore, illumination with blue light ignites a cyclic series of dark reactions including the typical intermediates I1, I2 and I2’, which suggests that it is functional although the recovery to the dark-adapted state was observed to be the slowest of any PYP. More interestingly, PYP from Salinibacter ruber contains an unusual 31-residue N-terminal extension which appears to be disordered relative to the remainder of the protein and which induces a unique dimerization of the photosensor with no precedents described before with any of the other published PYPs. Truncation of the N-terminal extension does not seem to influence the photochemical properties, and no structural motif or functional relevance towards signaling could thus far be established. PYP can also be part of multi-domain proteins such as Ppr from the phototroph Rhodospirillum centenum, where it forms the N-terminal domain that is followed by a central bacteriophytochrome (Bph) domain and by a C-terminal histidine kinase domain. The PYP domain acts as a blue-light switch reversing the effects of red light on the Bph domain, resulting in a light-regulated histidine kinase activity of Ppr. Comparative proteomics of wild-type Rh. centenum relative to a ppr gene deletion mutant revealed complex alterations in response to actinic blue- (390 - 510 nm) and red- (>600 nm) light conditions during photosynthetic growth. Differentially regulated proteins provide indications that the Ppr-mediated photoresponse involves an increased acetyl-CoA pool causing a shift in the lipid metabolism in favor of polyketide biosynthesis. However, the nature of this adaptation remains unclear and requires further study.","abstract_has_math":false,"creators":["Memmi, Samy"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":["Van Beeumen, J"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2008,"date_issued":"2008","date_published":"2008","updated_at":"2026-07-24T02:22:52Z","subjects":[],"languages":["und"],"rights":["info:eu-repo/semantics/openAccess"],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["https://biblio.ugent.be/publication/469245","http://doi.org/1854/10880","https://biblio.ugent.be/publication/469245/file/4334709"],"render_values":[{"text":"https://biblio.ugent.be/publication/469245","href":"https://biblio.ugent.be/publication/469245","code":true},{"text":"http://doi.org/1854/10880","href":"http://doi.org/1854/10880","code":true},{"text":"https://biblio.ugent.be/publication/469245/file/4334709","href":"https://biblio.ugent.be/publication/469245/file/4334709","code":true}]}]},"links":{"outbound_url":"http://hdl.handle.net/1854/LU-469245","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Van Beeumen, J"]},{"key":"dc:creator","label":"Author","values":["Memmi, Samy"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2008"]},{"key":"dc:type","label":"Dc Type","values":["dissertation","info:eu-repo/semantics/doctoralThesis","info:eu-repo/semantics/publishedVersion"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["und"]},{"key":"dc:rights","label":"Dc Rights","values":["info:eu-repo/semantics/openAccess"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://biblio.ugent.be/publication/469245","http://hdl.handle.net/1854/LU-469245","http://doi.org/1854/10880","https://biblio.ugent.be/publication/469245/file/4334709"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["The family of blue-light absorbing Photoactive Yellow Proteins (PYPs) has become an attractive model system to study the molecular events related to light perception. PYP covalently binds a p-hydroxycinnamic acid chromophore, which is fine-tuned for efficient light absorption and initiates a photocycle by a trans to cis isomerization. PYPs were originally discovered in a number of halophilic proteobacteria, but the pyp gene distribution actually spans a wider spectrum of both phototrophic as well as non-photosynthetic bacteria. PYP from Salinibacter ruber is shown to be the first example of a truly halophilic PYP that is stabilized by ionic strength. Furthermore, illumination with blue light ignites a cyclic series of dark reactions including the typical intermediates I1, I2 and I2’, which suggests that it is functional although the recovery to the dark-adapted state was observed to be the slowest of any PYP. More interestingly, PYP from Salinibacter ruber contains an unusual 31-residue N-terminal extension which appears to be disordered relative to the remainder of the protein and which induces a unique dimerization of the photosensor with no precedents described before with any of the other published PYPs. Truncation of the N-terminal extension does not seem to influence the photochemical properties, and no structural motif or functional relevance towards signaling could thus far be established. PYP can also be part of multi-domain proteins such as Ppr from the phototroph Rhodospirillum centenum, where it forms the N-terminal domain that is followed by a central bacteriophytochrome (Bph) domain and by a C-terminal histidine kinase domain. The PYP domain acts as a blue-light switch reversing the effects of red light on the Bph domain, resulting in a light-regulated histidine kinase activity of Ppr. Comparative proteomics of wild-type Rh. centenum relative to a ppr gene deletion mutant revealed complex alterations in response to actinic blue- (390 - 510 nm) and red- (>600 nm) light conditions during photosynthetic growth. Differentially regulated proteins provide indications that the Ppr-mediated photoresponse involves an increased acetyl-CoA pool causing a shift in the lipid metabolism in favor of polyketide biosynthesis. However, the nature of this adaptation remains unclear and requires further study."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Towards unveiling the Photoactive Yellow Proteins: characterization of a halophilic member and a proteomic approach to study light responses"]}]}],"canonical_facts":{"dc:contributor":["Van Beeumen, J"],"dc:creator":["Memmi, Samy"],"dc:date":["2008"],"dc:description":["The family of blue-light absorbing Photoactive Yellow Proteins (PYPs) has become an attractive model system to study the molecular events related to light perception. PYP covalently binds a p-hydroxycinnamic acid chromophore, which is fine-tuned for efficient light absorption and initiates a photocycle by a trans to cis isomerization. PYPs were originally discovered in a number of halophilic proteobacteria, but the pyp gene distribution actually spans a wider spectrum of both phototrophic as well as non-photosynthetic bacteria. PYP from Salinibacter ruber is shown to be the first example of a truly halophilic PYP that is stabilized by ionic strength. Furthermore, illumination with blue light ignites a cyclic series of dark reactions including the typical intermediates I1, I2 and I2’, which suggests that it is functional although the recovery to the dark-adapted state was observed to be the slowest of any PYP. More interestingly, PYP from Salinibacter ruber contains an unusual 31-residue N-terminal extension which appears to be disordered relative to the remainder of the protein and which induces a unique dimerization of the photosensor with no precedents described before with any of the other published PYPs. Truncation of the N-terminal extension does not seem to influence the photochemical properties, and no structural motif or functional relevance towards signaling could thus far be established. PYP can also be part of multi-domain proteins such as Ppr from the phototroph Rhodospirillum centenum, where it forms the N-terminal domain that is followed by a central bacteriophytochrome (Bph) domain and by a C-terminal histidine kinase domain. The PYP domain acts as a blue-light switch reversing the effects of red light on the Bph domain, resulting in a light-regulated histidine kinase activity of Ppr. Comparative proteomics of wild-type Rh. centenum relative to a ppr gene deletion mutant revealed complex alterations in response to actinic blue- (390 - 510 nm) and red- (>600 nm) light conditions during photosynthetic growth. Differentially regulated proteins provide indications that the Ppr-mediated photoresponse involves an increased acetyl-CoA pool causing a shift in the lipid metabolism in favor of polyketide biosynthesis. However, the nature of this adaptation remains unclear and requires further study."],"dc:format":["application/pdf"],"dc:identifier":["https://biblio.ugent.be/publication/469245","http://hdl.handle.net/1854/LU-469245","http://doi.org/1854/10880","https://biblio.ugent.be/publication/469245/file/4334709"],"dc:language":["und"],"dc:rights":["info:eu-repo/semantics/openAccess"],"dc:title":["Towards unveiling the Photoactive Yellow Proteins: characterization of a halophilic member and a proteomic approach to study light responses"],"dc:type":["dissertation","info:eu-repo/semantics/doctoralThesis","info:eu-repo/semantics/publishedVersion"]},"updated_at":"2026-07-24T02:22:52Z"}