{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T23:58:26Z","timestamp":1790812706857,"version":"4.1.0"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2017,8,29]],"date-time":"2017-08-29T00:00:00Z","timestamp":1503964800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The order Rhizobiales contains numerous agriculturally, biotechnologically, and medically important bacteria, including the rhizobia, and the genera Agrobacterium, Brucella, and Methylobacterium, among others. These organisms tend to be metabolically versatile, but there has been relatively little investigation into the regulation of their central carbon metabolic pathways. Here, RNA-sequencing and promoter fusion data are presented to show that the PckR protein is a key regulator of central carbon metabolism in Sinorhizobium meliloti; during growth with gluconeogenic substrates, PckR represses expression of the complete Entner\u2013Doudoroff glycolytic pathway and induces expression of the pckA and fbaB gluconeogenic genes. Electrophoretic mobility shift assays indicate that PckR binds an imperfect palindromic sequence that overlaps the promoter or transcriptional start site in the negatively regulated promoters, or is present in tandem upstream the promoter motifs in the positively regulated promoters. Genetic and in vitro electrophoretic mobility shift assay experiments suggest that elevated concentrations of a PckR effector ligand results in the dissociation of PckR from its target binding site, and evidence is presented that suggests phosphoenolpyruvate may function as the effector. Characterization of missense pckR alleles identified three conserved residues important for increasing the affinity of PckR for its cognate effector molecule. Bioinformatics analyses illustrates that PckR is limited to a narrow phylogenetic range consisting of the Rhizobiaceae, Phyllobacteriaceae, Brucellaceae, and Bartonellaceae families. These data provide novel insights into the regulation of the core carbon metabolic pathways of this pertinent group of \u03b1-proteobacteria.<\/jats:p>","DOI":"10.1534\/genetics.117.300212","type":"journal-article","created":{"date-parts":[[2017,8,30]],"date-time":"2017-08-30T01:00:27Z","timestamp":1504054827000},"page":"961-974","source":"Crossref","is-referenced-by-count":20,"title":["A Key Regulator of the Glycolytic and Gluconeogenic Central Metabolic Pathways in <i>Sinorhizobium meliloti<\/i>"],"prefix":"10.1093","volume":"207","author":[{"given":"George C","family":"diCenzo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zahed","family":"Muhammed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Magne","family":"\u00d8ster\u00e5s","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shelley A P","family":"O\u2019Brien","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Turlough M","family":"Finan","sequence":"additional","affiliation":[{"name":"Department of Biology , McMaster University, Hamilton, Ontario L8S 4K1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,8,29]]},"reference":[{"key":"2022110414543320100_bib1","doi-asserted-by":"crossref","first-page":"9716","DOI":"10.1073\/pnas.0305659101","article-title":"The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae.","volume":"101","author":"Alsmark","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2022110414543320100_bib2","first-page":"28","article-title":"Fitting a mixture model by expectation maximization to discover motifs in biopolymers.","volume":"2","author":"Bailey","year":"1994","journal-title":"Proc. Int. Conf. Intell. Syst. Mol. Biol."},{"key":"2022110414543320100_bib3","doi-asserted-by":"crossref","first-page":"W202","DOI":"10.1093\/nar\/gkp335","article-title":"MEME SUITE: tools for motif discovery and searching.","volume":"37","author":"Bailey","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2022110414543320100_bib4","doi-asserted-by":"crossref","first-page":"5396","DOI":"10.1128\/AEM.00196-09","article-title":"Metabolic capacity of Sinorhizobium (Ensifer) meliloti strains as determined by phenotype MicroArray analysis.","volume":"75","author":"Biondi","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"2022110414543320100_bib5","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/S0378-1119(97)00014-0","article-title":"Antibiotic resistance gene cassettes derived from the omega interposon for use in E. coli and Streptomyces.","volume":"190","author":"Blondelet-Rouault","year":"1997","journal-title":"Gene"},{"key":"2022110414543320100_bib6","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1007\/BF00414724","article-title":"Dicarboxylic acid transport in Rhizobium meliloti: isolation of mutants and cloning of dicarboxylic acid transport genes.","volume":"144","author":"Bolton","year":"1986","journal-title":"Arch. Microbiol."},{"key":"2022110414543320100_bib7","doi-asserted-by":"crossref","first-page":"5385","DOI":"10.1128\/JB.184.19.5385-5392.2002","article-title":"Control of inducer accumulation plays a key role in succinate-mediated catabolite repression in Sinorhizobium meliloti.","volume":"184","author":"Bringhurst","year":"2002","journal-title":"J. Bacteriol."},{"key":"2022110414543320100_bib8","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.","volume":"25","author":"Capella-Guti\u00e9rrez","year":"2009","journal-title":"Bioinformatics"},{"key":"2022110414543320100_bib9","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1111\/j.1365-2958.2010.07198.x","article-title":"FeuN, a novel modulator of two-component signalling identified in Sinorhizobium meliloti.","volume":"77","author":"Carlyon","year":"2010","journal-title":"Mol. Microbiol."},{"key":"2022110414543320100_bib10","doi-asserted-by":"crossref","first-page":"1853","DOI":"10.1099\/ijs.0.02644-0","article-title":"Fulvimarina pelagi gen. nov., sp. nov., a marine bacterium that forms a deep evolutionary lineage of descent in the order \u201cRhizobiales\u201d.","volume":"53","author":"Cho","year":"2003","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"2022110414543320100_bib11","doi-asserted-by":"crossref","first-page":"7156","DOI":"10.1128\/AEM.01397-06","article-title":"An integrated approach to functional genomics: construction of a novel reporter gene fusion library for Sinorhizobium meliloti.","volume":"72","author":"Cowie","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"2022110414543320100_bib12","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1099\/ijs.0.02359-0","article-title":"Aurantimonas coralicida gen. nov., sp. nov., the causative agent of white plague type II on Caribbean scleractinian corals.","volume":"53","author":"Denner","year":"2003","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"2022110414543320100_bib13","doi-asserted-by":"crossref","first-page":"e1004742","DOI":"10.1371\/journal.pgen.1004742","article-title":"Examination of prokaryotic multipartite genome evolution through experimental genome reduction.","volume":"10","author":"diCenzo","year":"2014","journal-title":"PLoS Genet."},{"key":"2022110414543320100_bib14","doi-asserted-by":"crossref","first-page":"12219","DOI":"10.1038\/ncomms12219","article-title":"Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti.","volume":"7","author":"diCenzo","year":"2016","journal-title":"Nat. Commun."},{"key":"2022110414543320100_bib15","doi-asserted-by":"crossref","first-page":"2534","DOI":"10.1111\/1462-2920.13221","article-title":"Genomic resources for identification of the minimal N2-fixing symbiotic genome.","volume":"18","author":"diCenzo","year":"2016","journal-title":"Environ. Microbiol."},{"key":"2022110414543320100_bib16"},{"key":"2022110414543320100_bib17","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1111\/j.1365-2958.1993.tb01177.x","article-title":"NAD+-dependent malic enzyme of Rhizobium meliloti is required for symbiotic nitrogen fixation.","volume":"7","author":"Driscoll","year":"1993","journal-title":"Mol. Microbiol."},{"key":"2022110414543320100_bib18","doi-asserted-by":"crossref","first-page":"2224","DOI":"10.1128\/jb.178.8.2224-2231.1996","article-title":"NADP+-dependent malic enzyme of Rhizobium meliloti.","volume":"178","author":"Driscoll","year":"1996","journal-title":"J. Bacteriol."},{"key":"2022110414543320100_bib19","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1099\/00221287-143-2-489","article-title":"Properties of NAD+- and NADP+-dependent malic enzymes of Rhizobium (Sinorhizobium) meliloti and differential expression of their genes in nitrogen-fixing bacteroids.","volume":"143","author":"Driscoll","year":"1997","journal-title":"Microbiology"},{"key":"2022110414543320100_bib20","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1016\/S0168-9525(97)01347-4","article-title":"Searching for patterns in genomic data.","volume":"13","author":"Dsouza","year":"1997","journal-title":"Trends Genet."},{"key":"2022110414543320100_bib21","first-page":"205","article-title":"A new generation of homology search tools based on probabilistic inference.","volume":"23","author":"Eddy","year":"2009","journal-title":"Genome Inform"},{"key":"2022110414543320100_bib22","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput.","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2022110414543320100_bib23","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1128\/jb.154.3.1403-1413.1983","article-title":"Symbiotic properties of C4-dicarboxylic acid transport mutants of Rhizobium leguminosarum.","volume":"154","author":"Finan","year":"1983","journal-title":"J. Bacteriol."},{"key":"2022110414543320100_bib24","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1128\/jb.159.1.120-124.1984","article-title":"General transduction in Rhizobium meliloti.","volume":"159","author":"Finan","year":"1984","journal-title":"J. Bacteriol."},{"key":"2022110414543320100_bib25","doi-asserted-by":"crossref","first-page":"3396","DOI":"10.1128\/jb.170.8.3396-3403.1988","article-title":"Mutants of Rhizobium meliloti defective in succinate metabolism.","volume":"170","author":"Finan","year":"1988","journal-title":"J. Bacteriol."},{"key":"2022110414543320100_bib26","doi-asserted-by":"crossref","first-page":"1581","DOI":"10.1128\/JB.187.5.1581-1590.2005","article-title":"Experimental identification and quantification of glucose metabolism in seven bacterial species.","volume":"187","author":"Fuhrer","year":"2005","journal-title":"J. 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Microbiol."},{"key":"2022110414543320100_bib32","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1046\/j.1365-2958.1998.01053.x","article-title":"Inducer exclusion in Escherichia coli by non-PTS substrates: the role of the PEP to pyruvate ratio in determining the phosphorylation state of enzyme IIAGlc.","volume":"30","author":"Hogema","year":"1998","journal-title":"Mol. Microbiol."},{"key":"2022110414543320100_bib33","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.bej.2005.05.012","article-title":"Dynamic responses of the intracellular metabolite concentrations of the wild type and pykA mutant Escherichia coli against pulse addition of glucose or NH3 under those limiting continuous cultures.","volume":"26","author":"Hoque","year":"2005","journal-title":"Biochem. Eng. 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Biol."},{"key":"2022110414543320100_bib36","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.02461-14","article-title":"CceR and AkgR regulate central carbon and energy metabolism in alphaproteobacteria.","volume":"6","author":"Imam","year":"2015","journal-title":"MBio"},{"key":"2022110414543320100_bib37","doi-asserted-by":"crossref","first-page":"5440","DOI":"10.1128\/AEM.00844-12","article-title":"One-step sequence- and ligation-independent cloning as a rapid and versatile cloning method for functional genomics studies.","volume":"78","author":"Jeong","year":"2012","journal-title":"Appl. Environ. Microbiol."},{"key":"2022110414543320100_bib38","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability.","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"2022110414543320100_bib39","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nprot.2015.053","article-title":"The Phyre2 web portal for protein modeling, prediction and analysis.","volume":"10","author":"Kelley","year":"2015","journal-title":"Nat. Protoc."},{"key":"2022110414543320100_bib40","doi-asserted-by":"crossref","first-page":"271","DOI":"10.4056\/sigs.3326772","article-title":"Complete genome sequence of Liberibacter crescens BT-1.","volume":"7","author":"Leonard","year":"2012","journal-title":"Stand. Genomic Sci."},{"key":"2022110414543320100_bib41","doi-asserted-by":"crossref","first-page":"1247","DOI":"10.1126\/science.271.5253.1247","article-title":"Crystal structure of the lactose operon repressor and its complexes with DNA and inducer.","volume":"271","author":"Lewis","year":"1996","journal-title":"Science"},{"key":"2022110414543320100_bib42","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.1128\/JB.01456-07","article-title":"Binding site determinants for the LysR-type transcriptional regulator PcaQ in the legume endosymbiont Sinorhizobium meliloti.","volume":"190","author":"MacLean","year":"2008","journal-title":"J. Bacteriol."},{"key":"2022110414543320100_bib43","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1111\/j.1365-2958.2004.04412.x","article-title":"The expression of a novel antisense gene mediates incompatibility within the large repABC family of \u03b1-proteobacterial plasmids.","volume":"55","author":"MacLellan","year":"2005","journal-title":"Mol. Microbiol."},{"key":"2022110414543320100_bib44","doi-asserted-by":"crossref","first-page":"1751","DOI":"10.1099\/mic.0.28743-0","article-title":"Promoter prediction in the rhizobia.","volume":"152","author":"MacLellan","year":"2006","journal-title":"Microbiology"},{"key":"2022110414543320100_bib45","first-page":"1","author":"Miller","year":"2010"},{"key":"2022110414543320100_bib46","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1128\/JB.01104-13","article-title":"Cell growth inhibition upon deletion of four toxin-antitoxin loci from the megaplasmids of Sinorhizobium meliloti.","volume":"196","author":"Milunovic","year":"2014","journal-title":"J. Bacteriol."},{"key":"2022110414543320100_bib47","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1186\/1471-2164-14-745","article-title":"RegPrecise 3.0\u2013a resource for genome-scale exploration of transcriptional regulation in bacteria.","volume":"14","author":"Novichkov","year":"2013","journal-title":"BMC Genomics"},{"key":"2022110414543320100_bib48","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.resmic.2006.11.003","article-title":"Inhibitory effect of phosphoenolpyruvate on glycolytic enzymes in Escherichia coli.","volume":"158","author":"Ogawa","year":"2007","journal-title":"Res. Microbiol."},{"key":"2022110414543320100_bib49","doi-asserted-by":"crossref","first-page":"1452","DOI":"10.1128\/jb.177.6.1452-1460.1995","article-title":"Molecular and expression analysis of the Rhizobium meliloti phosphoenolpyruvate carboxykinase (pckA) gene.","volume":"177","author":"\u00d8ster\u00e5s","year":"1995","journal-title":"J. Bacteriol."},{"key":"2022110414543320100_bib50","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.1093\/genetics\/147.4.1521","article-title":"Genetic analysis of mutations affecting pckA regulation in Rhizobium (Sinorhizobium) meliloti.","volume":"147","author":"\u00d8ster\u00e5s","year":"1997","journal-title":"Genetics"},{"key":"2022110414543320100_bib51","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2013a visualization system for exploratory research and analysis.","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"2022110414543320100_bib52","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1128\/JB.01115-08","article-title":"HPrK regulates succinate-mediated catabolite repression in the gram-negative symbiont Sinorhizobium meliloti.","volume":"191","author":"Pinedo","year":"2009","journal-title":"J. Bacteriol."},{"key":"2022110414543320100_bib53","doi-asserted-by":"crossref","first-page":"2947","DOI":"10.1128\/JB.01917-07","article-title":"Sinorhizobium meliloti mutants lacking phosphotransferase system enzyme HPr or EIIA are altered in diverse processes, including carbon metabolism, cobalt requirements, and succinoglycan production.","volume":"190","author":"Pinedo","year":"2008","journal-title":"J. Bacteriol."},{"key":"2022110414543320100_bib54","doi-asserted-by":"crossref","first-page":"3445","DOI":"10.1128\/JB.01707-06","article-title":"Characterization of Sinorhizobium meliloti triose phosphate isomerase genes.","volume":"189","author":"Poysti","year":"2007","journal-title":"J. Bacteriol."},{"key":"2022110414543320100_bib55","first-page":"e9490","article-title":"FastTree 2\u2013approximately maximum-likelihood trees for large alignments.","volume-title":"PLoS One","author":"Price","year":"2010"},{"key":"2022110414543320100_bib56","doi-asserted-by":"crossref","first-page":"10151","DOI":"10.1073\/pnas.93.19.10151","article-title":"Dual-function regulators: the cAMP receptor protein and the CytR regulator can act either to repress or to activate transcription depending on the context.","volume":"93","author":"Rasmussen","year":"1996","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2022110414543320100_bib57","doi-asserted-by":"crossref","first-page":"4284","DOI":"10.1073\/pnas.78.7.4284","article-title":"C4-dicarboxylate transport mutants of Rhizobium trifolii form ineffective nodules on Trifolium repens.","volume":"78","author":"Ronson","year":"1981","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2022110414543320100_bib58","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1093\/dnares\/dst014","article-title":"Next-generation annotation of prokaryotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011.","volume":"20","author":"Sallet","year":"2013","journal-title":"DNA Res."},{"key":"2022110414543320100_bib59","volume-title":"Molecular Cloning: A Laboratory Manual","author":"Sambrook","year":"1989"},{"key":"2022110414543320100_bib60","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1186\/1471-2164-14-156","article-title":"Global mapping of transcription start sites and promoter motifs in the symbiotic \u03b1-proteobacterium Sinorhizobium meliloti 1021.","volume":"14","author":"Schl\u00fcter","year":"2013","journal-title":"BMC Genomics"},{"key":"2022110414543320100_bib61","doi-asserted-by":"crossref","first-page":"1042","DOI":"10.1016\/j.jmb.2007.02.054","article-title":"Structural mechanism for the fine-tuning of CcpA function by the small molecule effectors glucose 6-phosphate and fructose 1,6-bisphosphate.","volume":"368","author":"Schumacher","year":"2007","journal-title":"J. Mol. Biol."},{"key":"2022110414543320100_bib62","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"2022110414543320100_bib63","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1146\/annurev.mi.39.100185.000513","article-title":"Carbon metabolism in Rhizobium species.","volume":"39","author":"Stowers","year":"1985","journal-title":"Annu. Rev. Microbiol."},{"key":"2022110414543320100_bib64","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.mib.2009.01.009","article-title":"Allostery in the LacI\/GalR family: variations on a theme.","volume":"12","author":"Swint-Kruse","year":"2009","journal-title":"Curr. Opin. Microbiol."},{"key":"2022110414543320100_bib65","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-014-0572-2","article-title":"De novo assembly of bacterial transcriptomes from RNA-seq data.","volume":"16","author":"Tjaden","year":"2015","journal-title":"Genome Biol."},{"key":"2022110414543320100_bib66","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1128\/jb.136.3.1197-1200.1978","article-title":"Catabolite-repression-like phenomenon in Rhizobium meliloti.","volume":"136","author":"Ucker","year":"1978","journal-title":"J. Bacteriol."},{"key":"2022110414543320100_bib67"},{"key":"2022110414543320100_bib68","doi-asserted-by":"crossref","first-page":"W469","DOI":"10.1093\/nar\/gkq406","article-title":"3DLigandSite: predicting ligand-binding sites using similar structures.","volume":"38","author":"Wass","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2022110414543320100_bib69","first-page":"e0138834","article-title":"CytR is a global positive regulator of competence, type VI secretion, and chitinases in Vibrio cholerae.","volume-title":"PLoS One","author":"Watve","year":"2015"},{"key":"2022110414543320100_bib70","doi-asserted-by":"crossref","first-page":"15869","DOI":"10.1016\/S0021-9258(19)49615-4","article-title":"A family of bacterial regulators homologous to Gal and Lac repressors.","volume":"267","author":"Weickert","year":"1992","journal-title":"J. Biol. 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