The CouPSTU and TarPQM transporters in Rhodopseudomonas palustris: redundant, promiscuous uptake systems for lignin-derived aromatic substrates
The biodegradation of lignin, one of the most abundant carbon compounds on Earth, has important biotechnological applications in the derivation of useful products from lignocellulosic wastes. The purple photosynthetic bacterium Rhodopseudomonas palustris is able to grow photoheterotrophically under...
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| description | The biodegradation of lignin, one of the most abundant carbon compounds on Earth, has important biotechnological applications in the derivation of useful products from lignocellulosic wastes. The purple photosynthetic bacterium Rhodopseudomonas palustris is able to grow photoheterotrophically under anaerobic conditions on a range of phenylpropeneoid lignin monomers, including coumarate, ferulate, caffeate, and cinnamate. RPA1789 (CouP) is the periplasmic binding-protein component of an ABC system (CouPSTU; RPA1789, RPA1791-1793), which has previously been implicated in the active transport of this class of aromatic substrate. Here, we show using both intrinsic tryptophan fluorescence and isothermal titration calorimetry that CouP binds a range of phenylpropeneoid ligands with K d values in the nanomolar range. The crystal structure of CouP with ferulate as the bound ligand shows H-bond interactions between the 4-OH group of the aromatic ring with His309 and Gln305. H-bonds are also made between the carboxyl group on the ferulate side chain and Arg197, Ser222, and Thr102. An additional transport system (TarPQM; RPA1782-1784), a member of the tripartite ATP-independent periplasmic (TRAP) transporter family, is encoded at the same locus as rpa1789 and several other genes involved in coumarate metabolism. We show that the periplasmic binding-protein of this system (TarP; RPA1782) also binds coumarate, ferulate, caffeate, and cinnamate with nanomolar K d values. Thus, we conclude that R. palustris uses two redundant but energetically distinct primary and secondary transporters that both employ high-affinity periplasmic binding-proteins to maximise the uptake of lignin-derived aromatic substrates from the environment. Our data provide a detailed thermodynamic and structural basis for understanding the interaction of lignin-derived aromatic substrates with proteins and will be of use in the further exploitation of the flexible metabolism of R. palustris for anaerobic aromatic biotransformations. |
| doi_str_mv | 10.1371/journal.pone.0059844 |
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The purple photosynthetic bacterium Rhodopseudomonas palustris is able to grow photoheterotrophically under anaerobic conditions on a range of phenylpropeneoid lignin monomers, including coumarate, ferulate, caffeate, and cinnamate. RPA1789 (CouP) is the periplasmic binding-protein component of an ABC system (CouPSTU; RPA1789, RPA1791-1793), which has previously been implicated in the active transport of this class of aromatic substrate. Here, we show using both intrinsic tryptophan fluorescence and isothermal titration calorimetry that CouP binds a range of phenylpropeneoid ligands with K d values in the nanomolar range. The crystal structure of CouP with ferulate as the bound ligand shows H-bond interactions between the 4-OH group of the aromatic ring with His309 and Gln305. H-bonds are also made between the carboxyl group on the ferulate side chain and Arg197, Ser222, and Thr102. An additional transport system (TarPQM; RPA1782-1784), a member of the tripartite ATP-independent periplasmic (TRAP) transporter family, is encoded at the same locus as rpa1789 and several other genes involved in coumarate metabolism. We show that the periplasmic binding-protein of this system (TarP; RPA1782) also binds coumarate, ferulate, caffeate, and cinnamate with nanomolar K d values. Thus, we conclude that R. palustris uses two redundant but energetically distinct primary and secondary transporters that both employ high-affinity periplasmic binding-proteins to maximise the uptake of lignin-derived aromatic substrates from the environment. Our data provide a detailed thermodynamic and structural basis for understanding the interaction of lignin-derived aromatic substrates with proteins and will be of use in the further exploitation of the flexible metabolism of R. palustris for anaerobic aromatic biotransformations.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0059844</identifier><identifier>PMID: 23555803</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Acids ; Active transport ; Amino Acid Sequence ; Anaerobic conditions ; Bacterial Proteins - metabolism ; Binding ; Biodegradation ; Biological Transport ; Biology ; Biotechnology ; Calorimetry ; Carbon compounds ; Carboxyl group ; Coding ; Crystal structure ; Crystallography, X-Ray ; Exploitation ; Fluorescence ; Gene Expression Regulation, Bacterial ; Genomics ; Haemophilus influenzae ; Hydrogen Bonding ; Ligands ; Lignin ; Lignin - metabolism ; Lignocellulose ; Membrane Transport Proteins - metabolism ; Metabolism ; Molecular biology ; Molecular Sequence Data ; Monomers ; Photosynthesis ; Protein Binding ; Protein Denaturation ; Protein Folding ; Proteins ; Rana palustris ; Rhodopseudomonas - metabolism ; Rhodopseudomonas palustris ; Sequence Homology, Amino Acid ; Spectrometry, Fluorescence ; Studies ; Substrates ; Titration ; Titration calorimetry ; Transport ; Tryptophan</subject><ispartof>PloS one, 2013-03, Vol.8 (3), p.e59844-e59844</ispartof><rights>2013 Salmon et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2013 Salmon et al 2013 Salmon et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c526t-a446468b6043aa792a2453c7007893fbeac4939356a773e50c6904107e5aee5d3</citedby><cites>FETCH-LOGICAL-c526t-a446468b6043aa792a2453c7007893fbeac4939356a773e50c6904107e5aee5d3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3610893/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3610893/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79569,79570</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23555803$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Salmon, Robert C</creatorcontrib><creatorcontrib>Cliff, Matthew J</creatorcontrib><creatorcontrib>Rafferty, John B</creatorcontrib><creatorcontrib>Kelly, David J</creatorcontrib><title>The CouPSTU and TarPQM transporters in Rhodopseudomonas palustris: redundant, promiscuous uptake systems for lignin-derived aromatic substrates</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The biodegradation of lignin, one of the most abundant carbon compounds on Earth, has important biotechnological applications in the derivation of useful products from lignocellulosic wastes. The purple photosynthetic bacterium Rhodopseudomonas palustris is able to grow photoheterotrophically under anaerobic conditions on a range of phenylpropeneoid lignin monomers, including coumarate, ferulate, caffeate, and cinnamate. RPA1789 (CouP) is the periplasmic binding-protein component of an ABC system (CouPSTU; RPA1789, RPA1791-1793), which has previously been implicated in the active transport of this class of aromatic substrate. Here, we show using both intrinsic tryptophan fluorescence and isothermal titration calorimetry that CouP binds a range of phenylpropeneoid ligands with K d values in the nanomolar range. The crystal structure of CouP with ferulate as the bound ligand shows H-bond interactions between the 4-OH group of the aromatic ring with His309 and Gln305. H-bonds are also made between the carboxyl group on the ferulate side chain and Arg197, Ser222, and Thr102. An additional transport system (TarPQM; RPA1782-1784), a member of the tripartite ATP-independent periplasmic (TRAP) transporter family, is encoded at the same locus as rpa1789 and several other genes involved in coumarate metabolism. We show that the periplasmic binding-protein of this system (TarP; RPA1782) also binds coumarate, ferulate, caffeate, and cinnamate with nanomolar K d values. Thus, we conclude that R. palustris uses two redundant but energetically distinct primary and secondary transporters that both employ high-affinity periplasmic binding-proteins to maximise the uptake of lignin-derived aromatic substrates from the environment. Our data provide a detailed thermodynamic and structural basis for understanding the interaction of lignin-derived aromatic substrates with proteins and will be of use in the further exploitation of the flexible metabolism of R. palustris for anaerobic aromatic biotransformations.</description><subject>Acids</subject><subject>Active transport</subject><subject>Amino Acid Sequence</subject><subject>Anaerobic conditions</subject><subject>Bacterial Proteins - metabolism</subject><subject>Binding</subject><subject>Biodegradation</subject><subject>Biological Transport</subject><subject>Biology</subject><subject>Biotechnology</subject><subject>Calorimetry</subject><subject>Carbon compounds</subject><subject>Carboxyl group</subject><subject>Coding</subject><subject>Crystal structure</subject><subject>Crystallography, X-Ray</subject><subject>Exploitation</subject><subject>Fluorescence</subject><subject>Gene Expression Regulation, Bacterial</subject><subject>Genomics</subject><subject>Haemophilus influenzae</subject><subject>Hydrogen Bonding</subject><subject>Ligands</subject><subject>Lignin</subject><subject>Lignin - metabolism</subject><subject>Lignocellulose</subject><subject>Membrane Transport Proteins - metabolism</subject><subject>Metabolism</subject><subject>Molecular biology</subject><subject>Molecular Sequence Data</subject><subject>Monomers</subject><subject>Photosynthesis</subject><subject>Protein Binding</subject><subject>Protein Denaturation</subject><subject>Protein Folding</subject><subject>Proteins</subject><subject>Rana palustris</subject><subject>Rhodopseudomonas - metabolism</subject><subject>Rhodopseudomonas palustris</subject><subject>Sequence Homology, Amino Acid</subject><subject>Spectrometry, Fluorescence</subject><subject>Studies</subject><subject>Substrates</subject><subject>Titration</subject><subject>Titration calorimetry</subject><subject>Transport</subject><subject>Tryptophan</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNptUttu1DAQjRCIlsIfILDECw9kseNb0gcktOJSqYgC22drNp7sZsnawY4r9Sv4ZbzstmoRT7Y8Z86cMz5F8ZzRGeOavd34FBwMs9E7nFEqm1qIB8Uxa3hVqoryh3fuR8WTGDcZxGulHhdHFZdS1pQfF78XayRzny5-LC4JOEsWEC6-fSFTABdHHyYMkfSOfF9768eIyfqtdxDJCEOKU-jjKQlok7PgpjdkDH7bxzb5FEkaJ_iJJF7HCbeRdD6QoV-53pUWQ3-FlkBGw9S3JKZl5oIJ49PiUQdDxGeH86S4_PhhMf9cnn_9dDZ_f162slJTCUIooeqlooID6KaCSkjeakp13fBuidCKhjdcKtCao6StaqhgVKMERGn5SfFyzzsOPprDLqNhnNOG1rIRGXG2R1gPGzOGfgvh2njozd8HH1YGQhY_oKlZhZ1CtWSVFFowwIq2XMvOcsE7qTPXu8O0tNyibdFlt8M90vsV16_Nyl8ZrhjNhjLB6wNB8L8Sxsns1ozDAA7zrrPuSuS_1Xw369U_0P-7E3tUG3yMAbtbMYyaXb5uuswuX-aQr9z24q6R26abQPE_YF7Q0A</recordid><startdate>20130328</startdate><enddate>20130328</enddate><creator>Salmon, Robert C</creator><creator>Cliff, Matthew J</creator><creator>Rafferty, John B</creator><creator>Kelly, David J</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</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>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PHGZM</scope><scope>PHGZT</scope><scope>PIMPY</scope><scope>PJZUB</scope><scope>PKEHL</scope><scope>PPXIY</scope><scope>PQEST</scope><scope>PQGLB</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20130328</creationdate><title>The CouPSTU and TarPQM transporters in Rhodopseudomonas palustris: redundant, promiscuous uptake systems for lignin-derived aromatic substrates</title><author>Salmon, Robert C ; Cliff, Matthew J ; Rafferty, John B ; Kelly, David J</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c526t-a446468b6043aa792a2453c7007893fbeac4939356a773e50c6904107e5aee5d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Acids</topic><topic>Active transport</topic><topic>Amino Acid Sequence</topic><topic>Anaerobic conditions</topic><topic>Bacterial Proteins - metabolism</topic><topic>Binding</topic><topic>Biodegradation</topic><topic>Biological Transport</topic><topic>Biology</topic><topic>Biotechnology</topic><topic>Calorimetry</topic><topic>Carbon compounds</topic><topic>Carboxyl group</topic><topic>Coding</topic><topic>Crystal structure</topic><topic>Crystallography, X-Ray</topic><topic>Exploitation</topic><topic>Fluorescence</topic><topic>Gene Expression Regulation, Bacterial</topic><topic>Genomics</topic><topic>Haemophilus influenzae</topic><topic>Hydrogen Bonding</topic><topic>Ligands</topic><topic>Lignin</topic><topic>Lignin - metabolism</topic><topic>Lignocellulose</topic><topic>Membrane Transport Proteins - metabolism</topic><topic>Metabolism</topic><topic>Molecular biology</topic><topic>Molecular Sequence Data</topic><topic>Monomers</topic><topic>Photosynthesis</topic><topic>Protein Binding</topic><topic>Protein Denaturation</topic><topic>Protein Folding</topic><topic>Proteins</topic><topic>Rana palustris</topic><topic>Rhodopseudomonas - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Salmon, Robert C</au><au>Cliff, Matthew J</au><au>Rafferty, John B</au><au>Kelly, David J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The CouPSTU and TarPQM transporters in Rhodopseudomonas palustris: redundant, promiscuous uptake systems for lignin-derived aromatic substrates</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2013-03-28</date><risdate>2013</risdate><volume>8</volume><issue>3</issue><spage>e59844</spage><epage>e59844</epage><pages>e59844-e59844</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The biodegradation of lignin, one of the most abundant carbon compounds on Earth, has important biotechnological applications in the derivation of useful products from lignocellulosic wastes. The purple photosynthetic bacterium Rhodopseudomonas palustris is able to grow photoheterotrophically under anaerobic conditions on a range of phenylpropeneoid lignin monomers, including coumarate, ferulate, caffeate, and cinnamate. RPA1789 (CouP) is the periplasmic binding-protein component of an ABC system (CouPSTU; RPA1789, RPA1791-1793), which has previously been implicated in the active transport of this class of aromatic substrate. Here, we show using both intrinsic tryptophan fluorescence and isothermal titration calorimetry that CouP binds a range of phenylpropeneoid ligands with K d values in the nanomolar range. The crystal structure of CouP with ferulate as the bound ligand shows H-bond interactions between the 4-OH group of the aromatic ring with His309 and Gln305. H-bonds are also made between the carboxyl group on the ferulate side chain and Arg197, Ser222, and Thr102. An additional transport system (TarPQM; RPA1782-1784), a member of the tripartite ATP-independent periplasmic (TRAP) transporter family, is encoded at the same locus as rpa1789 and several other genes involved in coumarate metabolism. We show that the periplasmic binding-protein of this system (TarP; RPA1782) also binds coumarate, ferulate, caffeate, and cinnamate with nanomolar K d values. Thus, we conclude that R. palustris uses two redundant but energetically distinct primary and secondary transporters that both employ high-affinity periplasmic binding-proteins to maximise the uptake of lignin-derived aromatic substrates from the environment. Our data provide a detailed thermodynamic and structural basis for understanding the interaction of lignin-derived aromatic substrates with proteins and will be of use in the further exploitation of the flexible metabolism of R. palustris for anaerobic aromatic biotransformations.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23555803</pmid><doi>10.1371/journal.pone.0059844</doi><oa>free_for_read</oa></addata></record> |
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| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Acids Active transport Amino Acid Sequence Anaerobic conditions Bacterial Proteins - metabolism Binding Biodegradation Biological Transport Biology Biotechnology Calorimetry Carbon compounds Carboxyl group Coding Crystal structure Crystallography, X-Ray Exploitation Fluorescence Gene Expression Regulation, Bacterial Genomics Haemophilus influenzae Hydrogen Bonding Ligands Lignin Lignin - metabolism Lignocellulose Membrane Transport Proteins - metabolism Metabolism Molecular biology Molecular Sequence Data Monomers Photosynthesis Protein Binding Protein Denaturation Protein Folding Proteins Rana palustris Rhodopseudomonas - metabolism Rhodopseudomonas palustris Sequence Homology, Amino Acid Spectrometry, Fluorescence Studies Substrates Titration Titration calorimetry Transport Tryptophan |
| title | The CouPSTU and TarPQM transporters in Rhodopseudomonas palustris: redundant, promiscuous uptake systems for lignin-derived aromatic substrates |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-21T20%3A54%3A15IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=The%20CouPSTU%20and%20TarPQM%20transporters%20in%20Rhodopseudomonas%20palustris:%20redundant,%20promiscuous%20uptake%20systems%20for%20lignin-derived%20aromatic%20substrates&rft.jtitle=PloS%20one&rft.au=Salmon,%20Robert%20C&rft.date=2013-03-28&rft.volume=8&rft.issue=3&rft.spage=e59844&rft.epage=e59844&rft.pages=e59844-e59844&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0059844&rft_dat=%3Cproquest_plos_%3E2949871901%3C/proquest_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1330908594&rft_id=info:pmid/23555803&rft_doaj_id=oai_doaj_org_article_812ef6e6b1254741ae20c375fd343f57&rfr_iscdi=true |