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myo-inositol and D-ribose ligand discrimination in an ABC periplasmic binding protein. J Bacteriol 2013; 195:2379-88. [PMID: 23504019 DOI: 10.1128/jb.00116-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The periplasmic binding protein (PBP) IbpA mediates the uptake of myo-inositol by the IatP-IatA ATP-binding cassette transmembrane transporter. We report a crystal structure of Caulobacter crescentus IbpA bound to myo-inositol at 1.45 Å resolution. This constitutes the first structure of a PBP bound to inositol. IbpA adopts a type I PBP fold consisting of two α-β lobes that surround a central hinge. A pocket positioned between the lobes contains the myo-inositol ligand, which binds with submicromolar affinity (0.76 ± 0.08 μM). IbpA is homologous to ribose-binding proteins and binds D-ribose with low affinity (50.8 ± 3.4 μM). On the basis of IbpA and ribose-binding protein structures, we have designed variants of IbpA with inverted binding specificity for myo-inositol and D-ribose. Five mutations in the ligand-binding pocket are sufficient to increase the affinity of IbpA for D-ribose by 10-fold while completely abolishing binding to myo-inositol. Replacement of ibpA with these mutant alleles unable to bind myo-inositol abolishes C. crescentus growth in medium containing myo-inositol as the sole carbon source. Neither deletion of ibpA nor replacement of ibpA with the high-affinity ribose binding allele affected C. crescentus growth on D-ribose as a carbon source, providing evidence that the IatP-IatA transporter is specific for myo-inositol. This study outlines the evolutionary relationship between ribose- and inositol-binding proteins and provides insight into the molecular basis upon which these two related, but functionally distinct, classes of periplasmic proteins specifically bind carbohydrate ligands.
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Rodionova IA, Leyn SA, Burkart MD, Boucher N, Noll KM, Osterman AL, Rodionov DA. Novel inositol catabolic pathway inThermotoga maritima. Environ Microbiol 2013; 15:2254-66. [DOI: 10.1111/1462-2920.12096] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 01/18/2013] [Accepted: 01/20/2013] [Indexed: 11/30/2022]
Affiliation(s)
| | - Semen A. Leyn
- A. A. Kharkevich Institute for Information Transmission Problems; Russian Academy of Sciences; Moscow; 127994; Russia
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry; University of California San Diego; La Jolla; CA; 92093; USA
| | - Nathalie Boucher
- Department of Molecular and Cell Biology; University of Connecticut; Storrs; CT; 06269; USA
| | - Kenneth M. Noll
- Department of Molecular and Cell Biology; University of Connecticut; Storrs; CT; 06269; USA
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Yoshida KI, Sanbongi A, Murakami A, Suzuki H, Takenaka S, Takami H. Three inositol dehydrogenases involved in utilization and interconversion of inositol stereoisomers in a thermophile, Geobacillus kaustophilus HTA426. Microbiology (Reading) 2012; 158:1942-1952. [DOI: 10.1099/mic.0.059980-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ken-ichi Yoshida
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Azusa Sanbongi
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Ayano Murakami
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Hirokazu Suzuki
- Organization of Advanced Science and Technology, Kobe University, Kobe 657-8501, Japan
| | - Shinji Takenaka
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Hideto Takami
- Microbial Genome Research Group, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 237-0061, Japan
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Genetic and computational identification of a conserved bacterial metabolic module. PLoS Genet 2008; 4:e1000310. [PMID: 19096521 PMCID: PMC2597717 DOI: 10.1371/journal.pgen.1000310] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Accepted: 11/17/2008] [Indexed: 11/23/2022] Open
Abstract
We have experimentally and computationally defined a set of genes that form a conserved metabolic module in the α-proteobacterium Caulobacter crescentus and used this module to illustrate a schema for the propagation of pathway-level annotation across bacterial genera. Applying comprehensive forward and reverse genetic methods and genome-wide transcriptional analysis, we (1) confirmed the presence of genes involved in catabolism of the abundant environmental sugar myo-inositol, (2) defined an operon encoding an ABC-family myo-inositol transmembrane transporter, and (3) identified a novel myo-inositol regulator protein and cis-acting regulatory motif that control expression of genes in this metabolic module. Despite being encoded from non-contiguous loci on the C. crescentus chromosome, these myo-inositol catabolic enzymes and transporter proteins form a tightly linked functional group in a computationally inferred network of protein associations. Primary sequence comparison was not sufficient to confidently extend annotation of all components of this novel metabolic module to related bacterial genera. Consequently, we implemented the Graemlin multiple-network alignment algorithm to generate cross-species predictions of genes involved in myo-inositol transport and catabolism in other α-proteobacteria. Although the chromosomal organization of genes in this functional module varied between species, the upstream regions of genes in this aligned network were enriched for the same palindromic cis-regulatory motif identified experimentally in C. crescentus. Transposon disruption of the operon encoding the computationally predicted ABC myo-inositol transporter of Sinorhizobium meliloti abolished growth on myo-inositol as the sole carbon source, confirming our cross-genera functional prediction. Thus, we have defined regulatory, transport, and catabolic genes and a cis-acting regulatory sequence that form a conserved module required for myo-inositol metabolism in select α-proteobacteria. Moreover, this study describes a forward validation of gene-network alignment, and illustrates a strategy for reliably transferring pathway-level annotation across bacterial species. More than 1,000 microbial genomes have been sequenced to date, containing millions of predicted genes. While the broad functional category of many of these individual genes can be reliably predicted using sequence homology, sequence information alone is often insufficient to assign a gene a specific cellular function. Closing this gap in our understanding of gene function will require tremendous experimental effort over a broad phylogenetic cross-section of model microbes, along with computational methods for high-confidence extrapolation of functional information from model organisms to other species. Here, we report the experimental identification of a novel genetic module in the model α-proteobacterium C. crescentus that controls transport and catabolism of the abundant environmental sugar myo-inositol. A combination of computational methods for probabilistic protein-network assignment and gene-network alignment were required to reliably extend the annotation of genes in this metabolic module to related bacterial genera. Our computational predictions of the operon encoding the ABC myo-inositol transporter and an essential enzyme for myo-inositol catabolism in S. meliloti were validated experimentally, demonstrating the feasibility of our method for high-confidence propagation of pathway-level annotation across species.
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Yoshida KI, Yamaguchi M, Morinaga T, Kinehara M, Ikeuchi M, Ashida H, Fujita Y. myo-Inositol Catabolism in Bacillus subtilis. J Biol Chem 2008; 283:10415-24. [DOI: 10.1074/jbc.m708043200] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Kawsar HI, Ohtani K, Okumura K, Hayashi H, Shimizu T. Organization and transcriptional regulation ofmyo-inositol operon inClostridium perfringens. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09601.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Yoshida KI, Yamaguchi M, Ikeda H, Omae K, Tsurusaki KI, Fujita Y. The fifth gene of the iol operon of Bacillus subtilis, iolE, encodes 2-keto-myo-inositol dehydratase. Microbiology (Reading) 2004; 150:571-580. [PMID: 14993306 DOI: 10.1099/mic.0.26768-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The myo-inositol catabolism pathway of Bacillus subtilis has not been fully characterized but was proposed to involve step-wise multiple reactions that finally yielded acetyl-CoA and dihydroxyacetone phosphate. It is known that the iolABCDEFGHIJ operon is responsible for the catabolism of inositol. IolG catalyses the first step of myo-inositol catabolism, the dehydrogenation of myo-inositol, producing 2-keto-myo-inositol (inosose). The second step was thought to be the dehydration of inosose. Genetic and biochemical analyses of the iol genes led to the identification of iolE, encoding the enzyme for the second step of inositol catabolism, inosose dehydratase. The reaction product of inosose dehydratase was identified as D-2,3-diketo-4-deoxy-epi-inositol.
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Affiliation(s)
- Ken-Ichi Yoshida
- Department of Biotechnology, Faculty of Life Science and Biotechnology, Fukuyama University, 985 Sanzo, Higashimura-cho, Fukuyama-shi, Hiroshima 729-0292, Japan
| | - Masanori Yamaguchi
- Central Research Laboratories, Hokko Chemical Industry Co., Ltd, 2165 Toda, Atsugi-shi, Kanagawa 243-0023, Japan
| | - Hideki Ikeda
- Department of Biotechnology, Faculty of Life Science and Biotechnology, Fukuyama University, 985 Sanzo, Higashimura-cho, Fukuyama-shi, Hiroshima 729-0292, Japan
| | - Kaoru Omae
- Department of Biotechnology, Faculty of Life Science and Biotechnology, Fukuyama University, 985 Sanzo, Higashimura-cho, Fukuyama-shi, Hiroshima 729-0292, Japan
| | - Ken-Ichi Tsurusaki
- Department of Environment and Information Science, Faculty of Human Culture and Sciences, Fukuyama University, 985 Sanzo, Higashimura-cho, Fukuyama-shi, Hiroshima 729-0292, Japan
| | - Yasutaro Fujita
- Department of Biotechnology, Faculty of Life Science and Biotechnology, Fukuyama University, 985 Sanzo, Higashimura-cho, Fukuyama-shi, Hiroshima 729-0292, Japan
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Yoshida KI, Yamamoto Y, Omae K, Yamamoto M, Fujita Y. Identification of two myo-inositol transporter genes of Bacillus subtilis. J Bacteriol 2002; 184:983-91. [PMID: 11807058 PMCID: PMC134797 DOI: 10.1128/jb.184.4.983-991.2002] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among hundreds of mutants constructed systematically by the Japanese groups participating in the functional analysis of the Bacillus subtilis genome project, we found that a mutant with inactivation of iolT (ydjK) exhibited a growth defect on myo-inositol as the sole carbon source. The putative product of iolT exhibits significant similarity with many bacterial sugar transporters in the databases. In B. subtilis, the iolABCDEFGHIJ and iolRS operons are known to be involved in inositol utilization, and its transcription is regulated by the IolR repressor and induced by inositol. Among the iol genes, iolF was predicted to encode an inositol transporter. Inactivation of iolF alone did not cause such an obvious growth defect on inositol as the iolT inactivation, while simultaneous inactivation of the two genes led to a more severe defect than the single iolT inactivation. Determination of inositol uptake by the mutants revealed that iolT inactivation almost completely abolished uptake, but uptake by IolF itself was slightly detectable. These results, as well as the K(m) and V(max) values for the IolT and IolF inositol transporters, indicated that iolT and iolF encode major and minor inositol transporters, respectively. Northern and primer extension analyses of iolT transcription revealed that the gene is monocistronically transcribed from a promoter likely recognized by final sigma(A) RNA polymerase and negatively regulated by IolR as well. The interaction between IolR and the iolT promoter region was analyzed by means of gel retardation and DNase I footprinting experiments, it being suggested that the mode of interaction is quite similar to that found for the promoter regions of the iol divergon.
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Affiliation(s)
- Ken-Ichi Yoshida
- Department of Biotechnology, Fukuyama University, Fukuyama, Hiroshima 729-0292, Japan
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Galbraith MP, Feng SF, Borneman J, Triplett EW, de Bruijn FJ, Rossbachl S. A functional myo-inositol catabolism pathway is essential for rhizopine utilization by Sinorhizobium meliloti. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 10):2915-2924. [PMID: 9802033 DOI: 10.1099/00221287-144-10-2915] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Rhizopine (L-3-O-methyl-scyllo-inosamine) is a symbiosis-specific compound found in alfalfa nodules induced by specific Sinorhizobium meliloti strains. It has been postulated that rhizobial strains able to synthesize and catabolize rhizopine gain a competitive advantage in the rhizosphere. The pathway of rhizopine degradation is analysed here. Since rhizopine is an inositol derivative, it was tested whether inositol catabolism is involved in rhizopine utilization. A genetic locus required for the catabolism of inositol as sole carbon source was cloned from S. meliloti. This locus was delimited by transposon Tn5 mutagenesis and its DNA sequence was determined. Based on DNA similarity studies and enzyme assays, this genetic region was shown to encode an S. meliloti myo-inositol dehydrogenase. Strains that harboured a mutation in the myo-inositol dehydrogenase gene (idhA) did not display myo-inositol dehydrogenase activity, were unable to utilize myo-inositol as sole carbon/energy source, and were unable to catabolize rhizopine. Thus, myo-inositol dehydrogenase activity is essential for rhizopine utilization in S. meliloti.
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Affiliation(s)
- Mark P Galbraith
- Department of Biological Sciences, Western, Michigan UniversityKalamazoo, MI 49008USA
| | - Szi Fei Feng
- Department of Biological Sciences, Western, Michigan UniversityKalamazoo, MI 49008USA
| | - James Borneman
- Department of Agronomy and Center for the Study of Nitrogen Fixation, University of Wisconsin- MadisonMadison, WI 53706USA
| | - Eric W Triplett
- Department of Agronomy and Center for the Study of Nitrogen Fixation, University of Wisconsin- MadisonMadison, WI 53706USA
| | - Frans J de Bruijn
- MSU-DOE Plant Research Laboratory, Department of Microbiology, NSF Center for Microbial Ecology, Michigan State UniversityEast Lansing, MI 48824USA
| | - Silvia Rossbachl
- Department of Biological Sciences, Western, Michigan UniversityKalamazoo, MI 49008USA
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Yoshida KI, Aoyama D, Ishio I, Shibayama T, Fujita Y. Organization and transcription of the myo-inositol operon, iol, of Bacillus subtilis. J Bacteriol 1997; 179:4591-8. [PMID: 9226270 PMCID: PMC179296 DOI: 10.1128/jb.179.14.4591-4598.1997] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Previous determination of the nucleotide sequence of the iol region of the Bacillus subtilis genome allowed us to predict the structure of the iol operon for myo-inositol catabolism, consisting of 10 iol genes (iolA to iouJ); iolG corresponds to idh, encoding myo-inositol 2-dehydrogenase (Idh). Primer extension analysis suggested that an inositol-inducible promoter for the iol operon (iol promoter) might be a promoter-like sequence in the 5' region of iolA, which is probably recognized by sigmaA. S1 nuclease analysis implied that a rho-independent terminator-like structure in the 3' region of iolJ might be a terminator for iol transcription. Disruption of the iol promoter prevented synthesis of the iol transcript as well as that of Idh, implying that the iol operon is most probably transcribed as an 11.5-kb mRNA containing the 10 iol genes. Immediately upstream of the iol operon, two genes (iolR and iolS) with divergent orientations to the iol operon were found. Disruption of iolR (but not iolS) caused constitutive synthesis of the iol transcript and Idh, indicating that the iolR gene encodes a transcription-negative regulator (presumably a repressor) for the iol operon. Northern and S1 nuclease analyses revealed that the iolRS genes were cotranscribed from another inositol-inducible promoter, which is probably recognized by sigmaA. The promoter assignments of the iol and iolRS operons were confirmed in vivo with a lacZ fusion integrated into the amyE locus.
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Affiliation(s)
- K I Yoshida
- Department of Biotechnology, Faculty of Engineering, Fukuyama University, Hiroshima, Japan
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Evidence for the existence of a novel enzyme system. myo-Inositol-1-phosphate dehydrogenase in Phaseolus aureus. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86751-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Deshusses J, Reber G. Myo-inositol transport in Aerobacter aerogenes. BIOCHIMICA ET BIOPHYSICA ACTA 1972; 274:598-605. [PMID: 5049009 DOI: 10.1016/0005-2736(72)90206-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Abstract
A mutant of Aerobacter aerogenes produces constitutively the series of enzymes that mediates the degradation of myo-inositol and which in the wildtype strain is inducible. When grown on l-histidine, the mutant forms the enzymes at a level approximately three times as high as that seen in the induced wild type. The enzymes appear to be coordinately regulated and are sensitive to catabolite repression. Unless repressed, the synthesis of these enzymes markedly retards the growth of the mutant.
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