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Revisiting Fur Regulon Leads to a Comprehensive Understanding of Iron and Fur Regulation
Iron is an essential element because it functions as a cofactor of many enzymes, but excess iron causes cell damage. Iron hemostasis in was transcriptionally maintained by the ferric uptake regulator (Fur). Despite having been studied extensively, the comprehensive physiological roles and mechanisms...
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Published in: | International journal of molecular sciences 2023-05, Vol.24 (10), p.9078 |
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description | Iron is an essential element because it functions as a cofactor of many enzymes, but excess iron causes cell damage. Iron hemostasis in
was transcriptionally maintained by the ferric uptake regulator (Fur). Despite having been studied extensively, the comprehensive physiological roles and mechanisms of Fur-coordinated iron metabolism still remain obscure. In this work, by integrating a high-resolution transcriptomic study of the Fur wild-type and knockout
K-12 strains in the presence or absence of iron with high-throughput ChIP-seq assay and physiological studies, we revisited the regulatory roles of iron and Fur systematically and discovered several intriguing features of Fur regulation. The size of the Fur regulon was expanded greatly, and significant discrepancies were observed to exist between the regulations of Fur on the genes under its direct repression and activation. Fur showed stronger binding strength to the genes under its repression, and genes that were repressed by Fur were more sensitive to Fur and iron regulation as compared to the genes that were activated by Fur. Finally, we found that Fur linked iron metabolism to many essential processes, and the systemic regulations of Fur on carbon metabolism, respiration, and motility were further validated or discussed. These results highlight how Fur and Fur-controlled iron metabolism affect many cellular processes in a systematic way. |
doi_str_mv | 10.3390/ijms24109078 |
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was transcriptionally maintained by the ferric uptake regulator (Fur). Despite having been studied extensively, the comprehensive physiological roles and mechanisms of Fur-coordinated iron metabolism still remain obscure. In this work, by integrating a high-resolution transcriptomic study of the Fur wild-type and knockout
K-12 strains in the presence or absence of iron with high-throughput ChIP-seq assay and physiological studies, we revisited the regulatory roles of iron and Fur systematically and discovered several intriguing features of Fur regulation. The size of the Fur regulon was expanded greatly, and significant discrepancies were observed to exist between the regulations of Fur on the genes under its direct repression and activation. Fur showed stronger binding strength to the genes under its repression, and genes that were repressed by Fur were more sensitive to Fur and iron regulation as compared to the genes that were activated by Fur. Finally, we found that Fur linked iron metabolism to many essential processes, and the systemic regulations of Fur on carbon metabolism, respiration, and motility were further validated or discussed. These results highlight how Fur and Fur-controlled iron metabolism affect many cellular processes in a systematic way.</description><identifier>ISSN: 1422-0067</identifier><identifier>ISSN: 1661-6596</identifier><identifier>EISSN: 1422-0067</identifier><identifier>DOI: 10.3390/ijms24109078</identifier><identifier>PMID: 37240425</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Bacterial Proteins - genetics ; Bacterial Proteins - metabolism ; Binding sites ; carbon metabolism ; E coli ; Enzymes ; Escherichia coli ; Escherichia coli - genetics ; Escherichia coli - metabolism ; Escherichia coli K12 - genetics ; ferric-uptake regulator ; Gene expression ; Gene Expression Regulation, Bacterial ; Gene silencing ; Genes ; Hemostasis ; Hemostatics ; Iron ; Iron - metabolism ; Metabolism ; motility ; Physiological aspects ; Proteins ; Regulations ; Regulon - genetics ; Repressor Proteins - genetics ; Repressor Proteins - metabolism ; Respiration ; RNA polymerase ; Transcriptomics</subject><ispartof>International journal of molecular sciences, 2023-05, Vol.24 (10), p.9078</ispartof><rights>COPYRIGHT 2023 MDPI AG</rights><rights>2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2023 by the authors. 2023</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c518t-acb1c4caed9ff609cf6e523dd361daef3c0904017a887b10609a5336d392e9a83</citedby><cites>FETCH-LOGICAL-c518t-acb1c4caed9ff609cf6e523dd361daef3c0904017a887b10609a5336d392e9a83</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2819457047/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2819457047?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,37013,44590,53791,53793,75126</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37240425$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hou, Chaofan</creatorcontrib><creatorcontrib>Liu, Lin</creatorcontrib><creatorcontrib>Ju, Xian</creatorcontrib><creatorcontrib>Xiao, Yunzhu</creatorcontrib><creatorcontrib>Li, Bingyu</creatorcontrib><creatorcontrib>You, Conghui</creatorcontrib><title>Revisiting Fur Regulon Leads to a Comprehensive Understanding of Iron and Fur Regulation</title><title>International journal of molecular sciences</title><addtitle>Int J Mol Sci</addtitle><description>Iron is an essential element because it functions as a cofactor of many enzymes, but excess iron causes cell damage. Iron hemostasis in
was transcriptionally maintained by the ferric uptake regulator (Fur). Despite having been studied extensively, the comprehensive physiological roles and mechanisms of Fur-coordinated iron metabolism still remain obscure. In this work, by integrating a high-resolution transcriptomic study of the Fur wild-type and knockout
K-12 strains in the presence or absence of iron with high-throughput ChIP-seq assay and physiological studies, we revisited the regulatory roles of iron and Fur systematically and discovered several intriguing features of Fur regulation. The size of the Fur regulon was expanded greatly, and significant discrepancies were observed to exist between the regulations of Fur on the genes under its direct repression and activation. Fur showed stronger binding strength to the genes under its repression, and genes that were repressed by Fur were more sensitive to Fur and iron regulation as compared to the genes that were activated by Fur. Finally, we found that Fur linked iron metabolism to many essential processes, and the systemic regulations of Fur on carbon metabolism, respiration, and motility were further validated or discussed. These results highlight how Fur and Fur-controlled iron metabolism affect many cellular processes in a systematic way.</description><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - metabolism</subject><subject>Binding sites</subject><subject>carbon metabolism</subject><subject>E coli</subject><subject>Enzymes</subject><subject>Escherichia coli</subject><subject>Escherichia coli - genetics</subject><subject>Escherichia coli - metabolism</subject><subject>Escherichia coli K12 - genetics</subject><subject>ferric-uptake regulator</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Bacterial</subject><subject>Gene silencing</subject><subject>Genes</subject><subject>Hemostasis</subject><subject>Hemostatics</subject><subject>Iron</subject><subject>Iron - metabolism</subject><subject>Metabolism</subject><subject>motility</subject><subject>Physiological aspects</subject><subject>Proteins</subject><subject>Regulations</subject><subject>Regulon - genetics</subject><subject>Repressor Proteins - genetics</subject><subject>Repressor Proteins - metabolism</subject><subject>Respiration</subject><subject>RNA polymerase</subject><subject>Transcriptomics</subject><issn>1422-0067</issn><issn>1661-6596</issn><issn>1422-0067</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNpdkt9rFDEQxxdRbK2--SwLvvjg1Umyv_Ik5bB6cCAUC76FXDLZ5thNzmT3oP-9c16tV8lDkslnvjOTmaJ4y-BSCAmf_HbMvGIgoe2eFees4nwB0LTPT85nxauctwBc8Fq-LM5EyyuoeH1e_LzBvc9-8qEvr-dU3mA_DzGUa9Q2l1MsdbmM4y7hHYbs91jeBospTzrYg0t05SoRTtd_7nryMbwuXjg9ZHzzsF8Ut9dffiy_Ldbfv66WV-uFqVk3LbTZMFMZjVY614A0rsGaC2tFw6xGJwwVVgFrdde1GwaE6FqIxgrJUepOXBSro66Neqt2yY863auovfpjiKlXOk3eDKh4W6NwRkoruqoB2wFnvLMcG2tNwzek9fmotZs3I1qDYUp6eCL69CX4O9XHvWKkJKkbpPDhQSHFXzPmSY0-GxwGHTDOWfGOAzAKfkj8_X_oNs4p0F8RxWRVt1C1RF0eqV5TBT64SIENLYujNzGg82S_amtO7QQAcvh4dDAp5pzQPabPQB0GRp0ODOHvTkt-hP9OiPgNPAq7VA</recordid><startdate>20230522</startdate><enddate>20230522</enddate><creator>Hou, Chaofan</creator><creator>Liu, Lin</creator><creator>Ju, Xian</creator><creator>Xiao, Yunzhu</creator><creator>Li, Bingyu</creator><creator>You, Conghui</creator><general>MDPI AG</general><general>MDPI</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>K9.</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>MBDVC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20230522</creationdate><title>Revisiting Fur Regulon Leads to a Comprehensive Understanding of Iron and Fur Regulation</title><author>Hou, Chaofan ; Liu, Lin ; Ju, Xian ; Xiao, Yunzhu ; Li, Bingyu ; You, Conghui</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c518t-acb1c4caed9ff609cf6e523dd361daef3c0904017a887b10609a5336d392e9a83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Bacterial Proteins - genetics</topic><topic>Bacterial Proteins - metabolism</topic><topic>Binding sites</topic><topic>carbon metabolism</topic><topic>E coli</topic><topic>Enzymes</topic><topic>Escherichia coli</topic><topic>Escherichia coli - genetics</topic><topic>Escherichia coli - metabolism</topic><topic>Escherichia coli K12 - genetics</topic><topic>ferric-uptake regulator</topic><topic>Gene expression</topic><topic>Gene Expression Regulation, Bacterial</topic><topic>Gene silencing</topic><topic>Genes</topic><topic>Hemostasis</topic><topic>Hemostatics</topic><topic>Iron</topic><topic>Iron - metabolism</topic><topic>Metabolism</topic><topic>motility</topic><topic>Physiological aspects</topic><topic>Proteins</topic><topic>Regulations</topic><topic>Regulon - genetics</topic><topic>Repressor Proteins - genetics</topic><topic>Repressor Proteins - metabolism</topic><topic>Respiration</topic><topic>RNA polymerase</topic><topic>Transcriptomics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hou, Chaofan</creatorcontrib><creatorcontrib>Liu, Lin</creatorcontrib><creatorcontrib>Ju, Xian</creatorcontrib><creatorcontrib>Xiao, Yunzhu</creatorcontrib><creatorcontrib>Li, Bingyu</creatorcontrib><creatorcontrib>You, Conghui</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>ProQuest Health and Medical</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>AUTh Library subscriptions: ProQuest Central</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>ProQuest Research Library</collection><collection>Research Library (Corporate)</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>Directory of Open Access Journals</collection><jtitle>International journal of molecular sciences</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hou, Chaofan</au><au>Liu, Lin</au><au>Ju, Xian</au><au>Xiao, Yunzhu</au><au>Li, Bingyu</au><au>You, Conghui</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Revisiting Fur Regulon Leads to a Comprehensive Understanding of Iron and Fur Regulation</atitle><jtitle>International journal of molecular sciences</jtitle><addtitle>Int J Mol Sci</addtitle><date>2023-05-22</date><risdate>2023</risdate><volume>24</volume><issue>10</issue><spage>9078</spage><pages>9078-</pages><issn>1422-0067</issn><issn>1661-6596</issn><eissn>1422-0067</eissn><abstract>Iron is an essential element because it functions as a cofactor of many enzymes, but excess iron causes cell damage. Iron hemostasis in
was transcriptionally maintained by the ferric uptake regulator (Fur). Despite having been studied extensively, the comprehensive physiological roles and mechanisms of Fur-coordinated iron metabolism still remain obscure. In this work, by integrating a high-resolution transcriptomic study of the Fur wild-type and knockout
K-12 strains in the presence or absence of iron with high-throughput ChIP-seq assay and physiological studies, we revisited the regulatory roles of iron and Fur systematically and discovered several intriguing features of Fur regulation. The size of the Fur regulon was expanded greatly, and significant discrepancies were observed to exist between the regulations of Fur on the genes under its direct repression and activation. Fur showed stronger binding strength to the genes under its repression, and genes that were repressed by Fur were more sensitive to Fur and iron regulation as compared to the genes that were activated by Fur. Finally, we found that Fur linked iron metabolism to many essential processes, and the systemic regulations of Fur on carbon metabolism, respiration, and motility were further validated or discussed. These results highlight how Fur and Fur-controlled iron metabolism affect many cellular processes in a systematic way.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>37240425</pmid><doi>10.3390/ijms24109078</doi><oa>free_for_read</oa></addata></record> |
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subjects | Bacterial Proteins - genetics Bacterial Proteins - metabolism Binding sites carbon metabolism E coli Enzymes Escherichia coli Escherichia coli - genetics Escherichia coli - metabolism Escherichia coli K12 - genetics ferric-uptake regulator Gene expression Gene Expression Regulation, Bacterial Gene silencing Genes Hemostasis Hemostatics Iron Iron - metabolism Metabolism motility Physiological aspects Proteins Regulations Regulon - genetics Repressor Proteins - genetics Repressor Proteins - metabolism Respiration RNA polymerase Transcriptomics |
title | Revisiting Fur Regulon Leads to a Comprehensive Understanding of Iron and Fur Regulation |
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