The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis
Summary By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al., ) this bacterium was considered a potential agent for environmental bioremediation of industrial waste and a good colonizer of the rhizosphere. However, neither the...
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| Published in | Environmental microbiology Vol. 18; no. 10; pp. 3403 - 3424 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Blackwell Publishing Ltd
01.10.2016
Wiley Subscription Services, Inc Society for Applied Microbiology and Wiley-Blackwell |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Summary
By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al., ) this bacterium was considered a potential agent for environmental bioremediation of industrial waste and a good colonizer of the rhizosphere. However, neither the annotation tools available at that time nor the scarcely available omics data—let alone metabolic modeling and other nowadays common systems biology approaches—allowed them to anticipate the astonishing capacities that are encoded in the genetic complement of this unique microorganism. In this work we have adopted a suite of state‐of‐the‐art genomic analysis tools to revisit the functional and metabolic information encoded in the chromosomal sequence of strain KT2440. We identified 242 new protein‐coding genes and re‐annotated the functions of 1548 genes, which are linked to almost 4900 PubMed references. Catabolic pathways for 92 compounds (carbon, nitrogen and phosphorus sources) that could not be accommodated by the previously constructed metabolic models were also predicted. The resulting examination not only accounts for some of the known stress tolerance traits known in P. putida but also recognizes the capacity of this bacterium to perform difficult redox reactions, thereby multiplying its value as a platform microorganism for industrial biotechnology. |
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| AbstractList | Summary
By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al., ) this bacterium was considered a potential agent for environmental bioremediation of industrial waste and a good colonizer of the rhizosphere. However, neither the annotation tools available at that time nor the scarcely available omics data—let alone metabolic modeling and other nowadays common systems biology approaches—allowed them to anticipate the astonishing capacities that are encoded in the genetic complement of this unique microorganism. In this work we have adopted a suite of state‐of‐the‐art genomic analysis tools to revisit the functional and metabolic information encoded in the chromosomal sequence of strain KT2440. We identified 242 new protein‐coding genes and re‐annotated the functions of 1548 genes, which are linked to almost 4900 PubMed references. Catabolic pathways for 92 compounds (carbon, nitrogen and phosphorus sources) that could not be accommodated by the previously constructed metabolic models were also predicted. The resulting examination not only accounts for some of the known stress tolerance traits known in P. putida but also recognizes the capacity of this bacterium to perform difficult redox reactions, thereby multiplying its value as a platform microorganism for industrial biotechnology. By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al., ) this bacterium was considered a potential agent for environmental bioremediation of industrial waste and a good colonizer of the rhizosphere. However, neither the annotation tools available at that time nor the scarcely available omics data-let alone metabolic modeling and other nowadays common systems biology approaches-allowed them to anticipate the astonishing capacities that are encoded in the genetic complement of this unique microorganism. In this work we have adopted a suite of state-of-the-art genomic analysis tools to revisit the functional and metabolic information encoded in the chromosomal sequence of strain KT2440. We identified 242 new protein-coding genes and re-annotated the functions of 1548 genes, which are linked to almost 4900 PubMed references. Catabolic pathways for 92 compounds (carbon, nitrogen and phosphorus sources) that could not be accommodated by the previously constructed metabolic models were also predicted. The resulting examination not only accounts for some of the known stress tolerance traits known in P. putida but also recognizes the capacity of this bacterium to perform difficult redox reactions, thereby multiplying its value as a platform microorganism for industrial biotechnology. By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al ., ) this bacterium was considered a potential agent for environmental bioremediation of industrial waste and a good colonizer of the rhizosphere. However, neither the annotation tools available at that time nor the scarcely available omics data—let alone metabolic modeling and other nowadays common systems biology approaches—allowed them to anticipate the astonishing capacities that are encoded in the genetic complement of this unique microorganism. In this work we have adopted a suite of state‐of‐the‐art genomic analysis tools to revisit the functional and metabolic information encoded in the chromosomal sequence of strain KT2440. We identified 242 new protein‐coding genes and re‐annotated the functions of 1548 genes, which are linked to almost 4900 PubMed references. Catabolic pathways for 92 compounds (carbon, nitrogen and phosphorus sources) that could not be accommodated by the previously constructed metabolic models were also predicted. The resulting examination not only accounts for some of the known stress tolerance traits known in P. putida but also recognizes the capacity of this bacterium to perform difficult redox reactions, thereby multiplying its value as a platform microorganism for industrial biotechnology. By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al., 2002) this bacterium was considered a potential agent for environmental bioremediation of industrial waste and a good colonizer of the rhizosphere. However, neither the annotation tools available at that time nor the scarcely available omics data—let alone metabolic modeling and other nowadays common systems biology approaches—allowed them to anticipate the astonishing capacities that are encoded in the genetic complement of this unique microorganism. In this work we have adopted a suite of state-of-the-art genomic analysis tools to revisit the functional and metabolic information encoded in the chromosomal sequence of strain KT2440. We identified 242 new protein-coding genes and re-annotated the functions of 1548 genes, which are linked to almost 4900 PubMed references. Catabolic pathways for 92 compounds (carbon, nitrogen and phosphorus sources) that could not be accommodated by the previously constructed metabolic models were also predicted. The resulting examination not only accounts for some of the known stress tolerance traits known in P. putida but also recognizes the capacity of this bacterium to perform difficult redox reactions, thereby multiplying its value as a platform microorganism for industrial biotechnology. Summary By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al., ) this bacterium was considered a potential agent for environmental bioremediation of industrial waste and a good colonizer of the rhizosphere. However, neither the annotation tools available at that time nor the scarcely available omics data--let alone metabolic modeling and other nowadays common systems biology approaches--allowed them to anticipate the astonishing capacities that are encoded in the genetic complement of this unique microorganism. In this work we have adopted a suite of state-of-the-art genomic analysis tools to revisit the functional and metabolic information encoded in the chromosomal sequence of strain KT2440. We identified 242 new protein-coding genes and re-annotated the functions of 1548 genes, which are linked to almost 4900 PubMed references. Catabolic pathways for 92 compounds (carbon, nitrogen and phosphorus sources) that could not be accommodated by the previously constructed metabolic models were also predicted. The resulting examination not only accounts for some of the known stress tolerance traits known in P. putida but also recognizes the capacity of this bacterium to perform difficult redox reactions, thereby multiplying its value as a platform microorganism for industrial biotechnology. |
| Author | Klenk, Hans-Peter Petersen, Jörn Rouy, Zoé Martins dos Santos, Vitor A. P. Danchin, Antoine Barbe, Valérie de Lorenzo, Víctor Médigue, Claudine Fraser, Claire Belda, Eugeni Sekowska, Agnieszka José Lopez-Sanchez, Maria Morgat, Anne Nikel, Pablo I. Cruveiller, Stéphane van Heck, Ruben G. A. Vallenet, David |
| Author_xml | – sequence: 1 givenname: Eugeni surname: Belda fullname: Belda, Eugeni email: eugeni.belda-cuesta@pasteur.fr, eugeni.belda-cuesta@pasteur.fr organization: Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, 2 rue Gaston Crémieux, 91057, Evry, France – sequence: 2 givenname: Ruben G. A. surname: van Heck fullname: van Heck, Ruben G. A. organization: Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, Building number 316, HB, 6703, Wageningen, The Netherlands – sequence: 3 givenname: Maria surname: José Lopez-Sanchez fullname: José Lopez-Sanchez, Maria organization: Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, 2 rue Gaston Crémieux, 91057, Evry, France – sequence: 4 givenname: Stéphane surname: Cruveiller fullname: Cruveiller, Stéphane organization: Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, 2 rue Gaston Crémieux, 91057, Evry, France – sequence: 5 givenname: Valérie surname: Barbe fullname: Barbe, Valérie organization: Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute, National Sequencing Center, 2 rue Gaston Crémieux, 91057, Evry, France – sequence: 6 givenname: Claire surname: Fraser fullname: Fraser, Claire organization: Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, MD, Baltimore, USA – sequence: 7 givenname: Hans-Peter surname: Klenk fullname: Klenk, Hans-Peter organization: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany – sequence: 8 givenname: Jörn surname: Petersen fullname: Petersen, Jörn organization: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany – sequence: 9 givenname: Anne surname: Morgat fullname: Morgat, Anne organization: Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CH-1206, Geneva, Switzerland – sequence: 10 givenname: Pablo I. surname: Nikel fullname: Nikel, Pablo I. organization: Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain – sequence: 11 givenname: David surname: Vallenet fullname: Vallenet, David organization: Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, 2 rue Gaston Crémieux, 91057, Evry, France – sequence: 12 givenname: Zoé surname: Rouy fullname: Rouy, Zoé organization: Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, 2 rue Gaston Crémieux, 91057, Evry, France – sequence: 13 givenname: Agnieszka surname: Sekowska fullname: Sekowska, Agnieszka organization: AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France – sequence: 14 givenname: Vitor A. P. surname: Martins dos Santos fullname: Martins dos Santos, Vitor A. P. organization: Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, Building number 316, HB, 6703, Wageningen, The Netherlands – sequence: 15 givenname: Víctor surname: de Lorenzo fullname: de Lorenzo, Víctor organization: Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain – sequence: 16 givenname: Antoine surname: Danchin fullname: Danchin, Antoine organization: AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France – sequence: 17 givenname: Claudine surname: Médigue fullname: Médigue, Claudine organization: Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, 2 rue Gaston Crémieux, 91057, Evry, France |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26913973$$D View this record in MEDLINE/PubMed https://cea.hal.science/cea-04541789$$DView record in HAL |
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| Cites_doi | 10.1111/j.1574-6976.2010.00249.x 10.1111/j.1365-2958.2009.06962.x 10.1111/1462-2920.12270 10.1074/jbc.M502585200 10.1111/j.1462-2920.2010.02331.x 10.1128/JB.01585-07 10.1139/cjm-46-1-59 10.1186/1472-6750-13-93 10.1093/emboj/16.19.5922 10.1093/nar/gks1193 10.1074/jbc.M801195200 10.1128/jb.170.7.3142-3149.1988 10.1093/nar/gku961 10.1046/j.1462-2920.2002.00370.x 10.1073/pnas.1501384112 10.1111/1758-2229.12223 10.1007/s12038-007-0055-7 10.1371/journal.pone.0098367 10.1128/AEM.65.11.4837-4847.1999 10.1111/j.1462-2920.2007.01464.x 10.1093/nar/gku1223 10.1016/B978-0-12-800143-1.00002-6 10.1111/1751-7915.12029 10.1038/sj.emboj.7601041 10.1093/nar/gks1194 10.1093/nar/gku1002 10.1073/pnas.062526999 10.1271/bbb.60.1720 10.1371/journal.pcbi.1001116 10.1128/JB.01393-07 10.1128/AEM.03565-12 10.1038/nature08480 10.15252/msb.20145697 10.1007/s00253-004-1862-5 10.1371/journal.pcbi.1000210 10.1007/s00203-005-0054-8 10.1074/jbc.274.53.37901 10.3389/fphar.2014.00231 10.1529/biophysj.106.084343 10.1002/biot.201000124 10.1038/nchembio768 10.1038/nprot.2011.308 10.1128/jb.178.10.2804-2812.1996 10.1186/1471-2164-13-69 10.1016/S0021-9258(19)50037-0 10.1074/jbc.M300815200 10.1006/jmbi.2000.4315 10.1111/1462-2920.12812 10.1093/nar/gku989 10.1111/1462-2920.13015 10.1093/nar/gkm160 10.1093/nar/25.5.955 10.1093/nar/gkp698 10.1371/journal.pgen.1000344 10.1128/jb.178.11.3362-3364.1996 10.1111/j.1462-2920.2004.00734.x 10.1074/jbc.M115.687749 10.1093/nar/gks1146 10.1002/pmic.200500329 10.1093/bioinformatics/btp352 10.1128/JB.180.13.3421-3431.1998 10.1038/nrmicro1021 10.1128/JB.184.10.2837-2840.2002 10.1073/pnas.0405375101 10.1093/nar/gkq1093 10.1093/bioinformatics/btt036 10.1038/nmeth.1701 10.1186/gb-2010-11-10-r106 10.1371/journal.pcbi.1003118 10.1128/JB.185.14.4233-4242.2003 10.1016/S0005-2736(99)00085-1 10.1016/j.tig.2012.11.001 10.1093/nar/gks1027 10.1016/j.bbamem.2005.09.010 10.1128/jb.178.6.1663-1670.1996 10.1093/nar/gkt900 10.1099/00221287-146-1-199 10.1023/A:1012275512136 10.1111/1758-2229.12090 10.1371/journal.pcbi.1000308 10.1046/j.1462-2920.2002.00368.x 10.1093/nar/gks1005 10.1046/j.1462-2920.2002.00366.x 10.1186/1471-2105-11-119 10.1093/database/bat059 10.1093/nar/gkt1103 10.1038/nchembio.1387 10.1016/0022-2836(81)90087-5 10.1128/JB.01178-10 10.1073/pnas.0601119103 10.1111/j.1462-2920.2010.02166.x 10.1128/jb.172.8.4339-4347.1990 10.1016/j.bbapap.2008.01.005 10.1007/978-1-61779-412-4_15 10.1101/gr.194201 10.1128/JB.183.2.644-653.2001 10.1046/j.1365-2958.2003.03547.x 10.1099/mic.0.028787-0 10.1016/S0021-9258(18)53913-2 10.1038/339157a0 10.1016/S0167-4781(97)00097-3 10.1111/j.1462-2920.2011.02430.x 10.4056/sigs.1794338 10.1093/oxfordjournals.molbev.a026410 10.1038/nrmicro3253 10.1111/j.1574-6976.2011.00269.x 10.1093/nar/gkq869 10.1093/nar/gkg847 10.1093/genetics/54.1.61 10.1371/journal.pcbi.1002540 10.1101/gr.186501 10.1016/S1369-5274(99)80030-7 10.1111/j.1365-2958.2010.07332.x 10.1111/1574-6976.12076 10.1152/ajpcell.00360.2004 10.1099/mic.0.044263-0 10.1128/JB.00968-07 10.1111/j.1365-2958.2010.07448.x 10.1371/journal.pone.0110038 10.1093/nar/gku1068 10.1128/JB.184.15.4246-4258.2002 10.1128/jb.174.3.889-898.1992 10.1016/j.pep.2003.07.006 10.1073/pnas.0802273105 10.1186/1752-0509-2-79 10.1016/S0167-4838(00)00214-4 10.1128/JB.00666-12 10.1093/bib/bbs058 10.1093/nar/gku1243 10.1093/nar/gkg590 10.1074/jbc.M109.033944 |
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| References | Parschat, K., Canne, C., Hüttermann, J., Kappl, R., and Fetzner, S. (2001) Xanthine dehydrogenase from Pseudomonas putida 86: specificity, oxidation-reduction potentials of its redox-active centers, and first EPR characterization. Biochim Biophys Acta 1544: 151-165. Lee, J.-H., Lee, K.-H., Kim, C.-G., Lee, S.-Y., Kim, G.-J., Park, Y.-H., and Chung, S.-O. (2005) Cloning and expression of a trehalose synthase from Pseudomonas stutzeri CJ38 in Escherichia coli for the production of trehalose. Appl Microbiol Biotechnol 68: 213-219. Sudom, A., Walters, R., Pastushok, L., Goldie, D., Prasad, L., Delbaere, L.T.J., and Goldie, H. (2003) Mechanisms of activation of phosphoenolpyruvate carboxykinase from Escherichia coli by Ca2+ and of desensitization by trypsin. J Bacteriol 185: 4233-4242. Scovill, W.H., Schreier, H.J., and Bayles, K.W. (1996) Identification and characterization of the pckA gene from Staphylococcus aureus. J Bacteriol 178: 3362-3364. Karp, P.D., Latendresse, M., and Caspi, R. (2011) The pathway tools pathway prediction algorithm. Stand Genom Sci 5: 424-429. Puchałka, J., Oberhardt, M.A., Godinho, M., Bielecka, A., Regenhardt, D., Timmis, K.N., et al. (2008) Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Comput Biol 4: e1000210. Wargo, M.J., and Hogan, D.A. (2009) Identification of genes required for Pseudomonas aeruginosa carnitine catabolism. Microbiology 155: 2411-2419. Smith, A.A.T., Belda, E., Viari, A., Medigue, C., and Vallenet, D. (2012) The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes. PLoS Comput Biol 8: e1002540. Kobayashi, K., Kato, M., Miura, Y., Kettoku, M., Komeda, T., and Iwamatsu, A. (1996) Gene analysis of trehalose-producing enzymes from hyperthermophilic archaea in Sulfolobales. Biosci Biotechnol Biochem 60: 1720-1723. Bocs, S., Cruveiller, S., Vallenet, D., Nuel, G., and Médigue, C. (2003) AMIGene: annotation of MIcrobial Genes. Nucleic Acids Res 31: 3723-3726. Carmel, O., Rahav-Manor, O., Dover, N., Shaanan, B., and Padan, E. (1997) The Na+-specific interaction between the LysR-type regulator, NhaR, and the nhaA gene encoding the Na+/H+ antiporter of Escherichia coli. EMBO J 16: 5922-5929. De Lorenzo, V. (2015) It's the metabolism, stupid! Environ Microbiol Rep 7: 18-19. Mitchell, A., Chang, H.-Y., Daugherty, L., Fraser, M., Hunter, S., Lopez, R., et al. (2015) The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res 43: D213-D221. Oberhardt, M.A., Puchałka, J., Martins dos Santos, V.A.P., and Papin, J.A. (2011) Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis. PLoS Comput Biol 7: e1001116. Venturi, V. (2003) Control of rpoS transcription in Escherichia coli and Pseudomonas: why so different? Mol Microbiol 49: 1-9. Bastard, K., Smith, A.A.T., Vergne-Vaxelaire, C., Perret, A., Zaparucha, A., De Melo-Minardi, R., et al. (2014) Revealing the hidden functional diversity of an enzyme family. Nat Chem Biol 10: 42-49. Molina-Henares, M.A., de la Torre, J., García-Salamanca, A., Molina-Henares, A.J., Herrera, M.C., Ramos, J.L., and Duque, E. (2010) Identification of conditionally essential genes for growth of Pseudomonas putida KT2440 on minimal medium through the screening of a genome-wide mutant library. Environ Microbiol 12: 1468-1485. Udaondo, Z., Molina, L., Segura, A., Duque, E., and Ramos, J.L. (2015) Analysis of the core genome and pangenome of Pseudomonas putida. Environ Microbiol, In press, DOI: 10.1111/1462-2920.13015. Kumar, V.S., and Maranas, C.D. (2009) GrowMatch: an automated method for reconciling in silico/in vivo growth predictions. PLoS Comput Biol 5: e1000308. Arias, S., Olivera, E.R., Arcos, M., Naharro, G., and Luengo, J.M. (2008) Genetic analyses and molecular characterization of the pathways involved in the conversion of 2-phenylethylamine and 2-phenylethanol into phenylacetic acid in Pseudomonas putida U. Environ Microbiol 10: 413-432. Silby, M.W., Winstanley, C., Godfrey, S.A.C., Levy, S.B., and Jackson, R.W. (2011) Pseudomonas genomes: diverse and adaptable. FEMS Microbiol Rev 35: 652-680. Dos Santos, V.A.P.M., Heim, S., Moore, E.R.B., Strätz, M., and Timmis, K.N. (2004) Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ Microbiol 6: 1264-1286. Pedruzzi, I., Rivoire, C., Auchincloss, A.H., Coudert, E., Keller, G., de Castro, E., et al. (2015) HAMAP in 2015: updates to the protein family classification and annotation system. Nucleic Acids Res 43: D1064-D1070. Hidese, R., Mihara, H., Kurihara, T., and Esaki, N. (2011) Escherichia coli dihydropyrimidine dehydrogenase is a novel NAD-dependent heterotetramer essential for the production of 5,6-dihydrouracil. J Bacteriol 193: 989-993. Hui, S., Silverman, J.M., Chen, S.S., Erickson, D.W., Basan, M., Wang, J., et al. (2015) Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria. Mol Syst Biol 11: e784. Schnackerz, K.D., and Dobritzsch, D. (2008) Amidohydrolases of the reductive pyrimidine catabolic pathway purification, characterization, structure, reaction mechanisms and enzyme deficiency. Biochim Biophys Acta 1784: 431-444. De Smet, K.A., Weston, A., Brown, I.N., Young, D.B., and Robertson, B.D. (2000) Three pathways for trehalose biosynthesis in mycobacteria. Microbiology 146: 199-208. Morgat, A., Axelsen, K.B., Lombardot, T., Alcántara, R., Aimo, L., Zerara, M., et al. (2015) Updates in Rhea-a manually curated resource of biochemical reactions. Nucleic Acids Res 43: D459-D464. Golovan, S., Wang, G., Zhang, J., and Forsberg, C.W. (2000) Characterization and overproduction of the Escherichia coli appA encoded bifunctional enzyme that exhibits both phytase and acid phosphatase activities. Can J Microbiol 46: 59-71. Smith, L.T., Pocard, J.A., Bernard, T., and Le Rudulier, D. (1988) Osmotic control of glycine betaine biosynthesis and degradation in Rhizobium meliloti. J Bacteriol 170: 3142-3149. Tormo, A., Almirón, M., and Kolter, R. (1990) surA, an Escherichia coli gene essential for survival in stationary phase. J Bacteriol 172: 4339-4347. Kaushik, J.K., and Bhat, R. (2003) Why is trehalose an exceptional protein stabilizer? An analysis of the thermal stability of proteins in the presence of the compatible osmolyte trehalose. J Biol Chem 278: 26458-26465. Hastings, J., de Matos, P., Dekker, A., Ennis, M., Harsha, B., Kale, N., et al. (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res 41: D456-D463. Foster, J.W. (1999) When protons attack: microbial strategies of acid adaptation. Curr Opin Microbiol 2: 170-174. Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C.A., et al. (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 42: D459-D471. Brett, C.L., Donowitz, M., and Rao, R. (2005) Evolutionary origins of eukaryotic sodium/proton exchangers. Am J Physiol Cell Physiol 288: C223-C239. Gralla, J.D., and Vargas, D.R. (2006) Potassium glutamate as a transcriptional inhibitor during bacterial osmoregulation. EMBO J 25: 1515-1521. Ramos-González, M.I., and Molin, S. (1998) Cloning, sequencing, and phenotypic characterization of the rpoS gene from Pseudomonas putida KT2440. J Bacteriol 180: 3421-3431. Winsor, G.L., Lam, D.K.W., Fleming, L., Lo, R., Whiteside, M.D., Yu, N.Y., et al. (2011) Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res 39: D596-D600. Nogales, J., Canales, A., Jiménez-Barbero, J., Serra, B., Pingarrón, J.M., García, J.L., and Díaz, E. (2011) Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Mol Microbiol 79: 359-374. Osterman, A. (2006) A hidden metabolic pathway exposed. Proc Natl Acad Sci U S A 103: 5637-5638. Smith, T.F., and Waterman, M.S. (1981) Identification of common molecular subsequences. J Mol Biol 147: 195-197. Anders, S., and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106. Acevedo-Rocha, C.G., Fang, G., Schmidt, M., Ussery, D.W., and Danchin, A. (2013) From essential to persistent genes: a functional approach to constructing synthetic life. Trends Genet 29: 273-279. La Rosa, R., Nogales, J., and Rojo, F. (2015) The Crc/CrcZ-CrcY global regulatory system helps the integration of gluconeogenic and glycolytic metabolism in Pseudomonas putida. Environ Microbiol 17: 3362-3378. Mikoulinskaia, G.V., Zimin, A.A., Feofanov, S.A., and Miroshnikov, A.I. (2004) Identification, cloning, and expression of bacteriophage T5 dnk gene encoding a broad specificity deoxyribonucleoside monophosphate kinase (EC 2.7.4.13). Protein Expr Purif 33: 166-175. West, T.P. (2001) Pyrimidine base catabolism in Pseudomonas putida biotype B. Antonie van Leeuwenhoek 80: 163-167. Bochner, B.R. (1989) Sleuthing out bacterial identities. Nature 339: 157-158. Médigue, C., Wong, B.C.-Y., Lin, M.C.-M., Bocs, S., and Danchin, A. (2002) The secE gene of Helicobacter pylori. J Bacteriol 184: 2837-2840. Pinner, E., Kotler, Y., Padan, E., and Schuldiner, S. (1993) Physiological role of nhaB, a specific Na+/H+ antiporter in Escherichia coli. J Biol Chem 268: 1729-1734. Nikel, P.I., Martínez-García, E., and de Lorenzo, V. (2014) Biotechnological domestication of pseudomonads using synthetic biology. Nat Rev Microbiol 12: 368-379. Barrett, T., Wilhite, S.E., Ledoux, P., Evangelista, C., Kim, I.F., Tomashevsky, M., et al. (2013) NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res 41: D991-D995. Frank, S., Klockgether, J., Hagendorf, P., Geffers, R., Schöck, U., Pohl, T., et al. (2011) Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray 2010; 12 2010; 11 2008; 190 2007; 189 1981; 147 2002; 99 2004; 6 2008; 105 2004; 2 2001; 1544 2012; 13 2001; 305 1966; 54 2003; 278 2013; 5 2011; 193 2013; 6 2013; 9 2005; 68 2004; 33 2000; 17 2013; 2013 2006; 25 2014; 16 2014; 15 1996; 60 2003; 49 2010; 5 2014; 12 2014; 10 2012; 813 1990; 172 1988; 170 1997; 25 1992; 267 2010; 285 2002; 4 2011; 79 2011; 6 2011; 5 2003; 31 2011; 8 2011; 7 2014; 43 2014; 42 2012; 194 2013; 79 1984; 1 2015; 112 2014; 38 2006; 185 2009; 461 2006; 103 2003; 185 2013; 29 2011; 157 2005; 1717 2001; 183 2000; 46 2009; 155 2011; 13 1999; 1420 2008; 4 2007; 32 2008; 2 2007; 35 2014; 64 2014; 5 2015; 290 2002; 184 2013; 13 2015; 43 1997; 16 2014; 9 2001; 11 1996; 178 2004; 101 1998; 180 2010; 78 2009; 25 2006; 90 2010; 75 2015; 17 1989; 339 2015; 11 2013; 41 2006; 6 1999; 65 2008; 10 2011; 35 1999; 2 2006; 2 1993; 268 2011; 39 1998; 1395 2015; 7 2008; 283 2001; 80 2005; 280 2008; 1784 2000; 146 1992; 174 2005; 288 1999; 274 2015 2009; 5 2009; 37 2012; 8 e_1_2_6_114_1 e_1_2_6_53_1 e_1_2_6_76_1 e_1_2_6_95_1 e_1_2_6_118_1 e_1_2_6_30_1 e_1_2_6_72_1 e_1_2_6_91_1 e_1_2_6_110_1 e_1_2_6_133_1 e_1_2_6_19_1 e_1_2_6_11_1 e_1_2_6_34_1 e_1_2_6_15_1 e_1_2_6_38_1 e_1_2_6_57_1 e_1_2_6_99_1 e_1_2_6_125_1 e_1_2_6_64_1 e_1_2_6_87_1 Rahav‐Manor O. (e_1_2_6_96_1) 1992; 267 e_1_2_6_106_1 e_1_2_6_129_1 e_1_2_6_41_1 e_1_2_6_60_1 e_1_2_6_83_1 e_1_2_6_121_1 e_1_2_6_102_1 e_1_2_6_9_1 e_1_2_6_5_1 e_1_2_6_49_1 e_1_2_6_22_1 e_1_2_6_45_1 e_1_2_6_26_1 e_1_2_6_68_1 e_1_2_6_73_1 e_1_2_6_54_1 e_1_2_6_117_1 e_1_2_6_31_1 e_1_2_6_50_1 e_1_2_6_92_1 Palleroni N.J. (e_1_2_6_90_1) 1984 e_1_2_6_132_1 e_1_2_6_113_1 e_1_2_6_35_1 e_1_2_6_12_1 e_1_2_6_39_1 e_1_2_6_77_1 e_1_2_6_16_1 e_1_2_6_58_1 e_1_2_6_84_1 e_1_2_6_42_1 e_1_2_6_105_1 e_1_2_6_128_1 e_1_2_6_65_1 e_1_2_6_80_1 e_1_2_6_109_1 e_1_2_6_61_1 e_1_2_6_120_1 e_1_2_6_101_1 e_1_2_6_124_1 e_1_2_6_6_1 e_1_2_6_23_1 e_1_2_6_2_1 e_1_2_6_27_1 e_1_2_6_46_1 e_1_2_6_69_1 e_1_2_6_51_1 e_1_2_6_74_1 e_1_2_6_97_1 e_1_2_6_116_1 e_1_2_6_32_1 e_1_2_6_70_1 e_1_2_6_93_1 e_1_2_6_131_1 e_1_2_6_112_1 e_1_2_6_13_1 e_1_2_6_36_1 e_1_2_6_59_1 e_1_2_6_17_1 e_1_2_6_55_1 e_1_2_6_78_1 e_1_2_6_62_1 e_1_2_6_85_1 e_1_2_6_104_1 e_1_2_6_43_1 e_1_2_6_127_1 e_1_2_6_81_1 e_1_2_6_20_1 e_1_2_6_108_1 e_1_2_6_100_1 e_1_2_6_123_1 e_1_2_6_7_1 e_1_2_6_24_1 e_1_2_6_3_1 e_1_2_6_66_1 e_1_2_6_89_1 e_1_2_6_28_1 e_1_2_6_47_1 e_1_2_6_52_1 e_1_2_6_98_1 e_1_2_6_115_1 e_1_2_6_75_1 e_1_2_6_10_1 e_1_2_6_94_1 e_1_2_6_119_1 e_1_2_6_71_1 e_1_2_6_130_1 e_1_2_6_111_1 e_1_2_6_14_1 e_1_2_6_33_1 e_1_2_6_18_1 e_1_2_6_56_1 e_1_2_6_37_1 e_1_2_6_79_1 e_1_2_6_103_1 e_1_2_6_126_1 e_1_2_6_63_1 e_1_2_6_86_1 e_1_2_6_21_1 e_1_2_6_107_1 e_1_2_6_40_1 e_1_2_6_82_1 Overhage J. (e_1_2_6_88_1) 1999; 65 e_1_2_6_122_1 e_1_2_6_8_1 e_1_2_6_4_1 e_1_2_6_25_1 e_1_2_6_48_1 e_1_2_6_29_1 e_1_2_6_44_1 e_1_2_6_67_1 |
| References_xml | – reference: Silby, M.W., Winstanley, C., Godfrey, S.A.C., Levy, S.B., and Jackson, R.W. (2011) Pseudomonas genomes: diverse and adaptable. FEMS Microbiol Rev 35: 652-680. – reference: Anders, S., and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106. – reference: Van Duuren, J.B.J.H., Puchałka, J., Mars, A.E., Bücker, R., Eggink, G., Wittmann, C., and dos Santos, V.A.P.M. (2013) Reconciling in vivo and in silico key biological parameters of Pseudomonas putida KT2440 during growth on glucose under carbon-limited condition. BMC Biotechnol 13: 93. – reference: Wu, X., Monchy, S., Taghavi, S., Zhu, W., Ramos, J., and van der Lelie, D. (2011) Comparative genomics and functional analysis of niche-specific adaptation in Pseudomonas putida. FEMS Microbiol Rev 35: 299-323. – reference: Bastard, K., Smith, A.A.T., Vergne-Vaxelaire, C., Perret, A., Zaparucha, A., De Melo-Minardi, R., et al. (2014) Revealing the hidden functional diversity of an enzyme family. Nat Chem Biol 10: 42-49. – reference: Nikel, P.I., Chavarría, M., Fuhrer, T., Sauer, U., and de Lorenzo, V. (2015) Pseudomonas putida KT2440 strain metabolizes glucose through a cycle formed by enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and pentose phosphate pathways. J Biol Chem 290: 25920-25932. – reference: Claudel-Renard, C., Chevalet, C., Faraut, T., and Kahn, D. (2003) Enzyme-specific profiles for genome annotation: PRIAM. Nucleic Acids Res 31: 6633-6639. – reference: Schnackerz, K.D., and Dobritzsch, D. (2008) Amidohydrolases of the reductive pyrimidine catabolic pathway purification, characterization, structure, reaction mechanisms and enzyme deficiency. Biochim Biophys Acta 1784: 431-444. – reference: Ramazzina, I., Cendron, L., Folli, C., Berni, R., Monteverdi, D., Zanotti, G., and Percudani, R. (2008) Logical identification of an allantoinase analog (puuE) recruited from polysaccharide deacetylases. J Biol Chem 283: 23295-23304. – reference: Ruhal, R., Kataria, R., and Choudhury, B. (2013) Trends in bacterial trehalose metabolism and significant nodes of metabolic pathway in the direction of trehalose accumulation. Microb Biotechnol 6: 493-502. – reference: Bertin, Y., Deval, C., de la Foye, A., Masson, L., Gannon, V., Harel, J., et al. (2014) The gluconeogenesis pathway is involved in maintenance of enterohaemorrhagic Escherichia coli O157:H7 in bovine intestinal content. PLoS One 9: e98367. – reference: Keseler, I.M., Mackie, A., Peralta-Gil, M., Santos-Zavaleta, A., Gama-Castro, S., Bonavides-Martínez, C., et al. (2013) EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res 41: D605-D612. – reference: Kim, J., Oliveros, J.C., Nikel, P.I., de Lorenzo, V., and Silva-Rocha, R. (2013) Transcriptomic fingerprinting of Pseudomonas putida under alternative physiological regimes. Environ Microbiol Rep 5: 883-891. – reference: Jiménez, J.I., Miñambres, B., García, J.L., and Díaz, E. (2002) Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ Microbiol 4: 824-841. – reference: De Lorenzo, V. (2015) It's the metabolism, stupid! Environ Microbiol Rep 7: 18-19. – reference: Lee, J.-H., Lee, K.-H., Kim, C.-G., Lee, S.-Y., Kim, G.-J., Park, Y.-H., and Chung, S.-O. (2005) Cloning and expression of a trehalose synthase from Pseudomonas stutzeri CJ38 in Escherichia coli for the production of trehalose. Appl Microbiol Biotechnol 68: 213-219. – reference: Lagesen, K., Hallin, P., Rødland, E.A., Staerfeldt, H.-H., Rognes, T., and Ussery, D.W. (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35: 3100-3108. – reference: Vallenet, D., Belda, E., Calteau, A., Cruveiller, S., Engelen, S., Lajus, A., et al. (2013) MicroScope-an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res 41: D636-D647. – reference: Ballal, A., Basu, B., and Apte, S.K. (2007) The Kdp-ATPase system and its regulation. J Biosci 32: 559-568. – reference: Karp, P.D., Latendresse, M., and Caspi, R. (2011) The pathway tools pathway prediction algorithm. Stand Genom Sci 5: 424-429. – reference: Médigue, C., Wong, B.C.-Y., Lin, M.C.-M., Bocs, S., and Danchin, A. (2002) The secE gene of Helicobacter pylori. J Bacteriol 184: 2837-2840. – reference: Jiménez, J.I., Canales, A., Jiménez-Barbero, J., Ginalski, K., Rychlewski, L., García, J.L., and Díaz, E. (2008) Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440. Proc Natl Acad Sci U S A 105: 11329-11334. – reference: Venturi, V. (2003) Control of rpoS transcription in Escherichia coli and Pseudomonas: why so different? Mol Microbiol 49: 1-9. – reference: Kaasen, I., Falkenberg, P., Styrvold, O.B., and Strøm, A.R. (1992) Molecular cloning and physical mapping of the otsBA genes, which encode the osmoregulatory trehalose pathway of Escherichia coli: evidence that transcription is activated by katF (AppR). J Bacteriol 174: 889-898. – reference: Kell, D.B., and Oliver, S.G. (2014) How drugs get into cells: tested and testable predictions to help discriminate between transporter-mediated uptake and lipoidal bilayer diffusion. Front Pharmacol 5: 231. – reference: Wargo, M.J., and Hogan, D.A. (2009) Identification of genes required for Pseudomonas aeruginosa carnitine catabolism. Microbiology 155: 2411-2419. – reference: Rkenes, T.P., Lamark, T., and Strøm, A.R. (1996) DNA-binding properties of the BetI repressor protein of Escherichia coli: the inducer choline stimulates BetI-DNA complex formation. J Bacteriol 178: 1663-1670. – reference: Ning, Z., Cox, A.J., and Mullikin, J.C. (2001) SSAHA: a fast search method for large DNA databases. Genome Res 11: 1725-1729. – reference: Nogales, J., Canales, A., Jiménez-Barbero, J., Serra, B., Pingarrón, J.M., García, J.L., and Díaz, E. (2011) Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Mol Microbiol 79: 359-374. – reference: Tormo, A., Almirón, M., and Kolter, R. (1990) surA, an Escherichia coli gene essential for survival in stationary phase. J Bacteriol 172: 4339-4347. – reference: Petersen, T.N., Brunak, S., von Heijne, G., and Nielsen, H. (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8: 785-786. – reference: Kaushik, J.K., and Bhat, R. (2003) Why is trehalose an exceptional protein stabilizer? An analysis of the thermal stability of proteins in the presence of the compatible osmolyte trehalose. J Biol Chem 278: 26458-26465. – reference: Arias, S., Olivera, E.R., Arcos, M., Naharro, G., and Luengo, J.M. (2008) Genetic analyses and molecular characterization of the pathways involved in the conversion of 2-phenylethylamine and 2-phenylethanol into phenylacetic acid in Pseudomonas putida U. Environ Microbiol 10: 413-432. – reference: Schellenberger, J., Que, R., Fleming, R.M.T., Thiele, I., Orth, J.D., Feist, A.M., et al. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6: 1290-1307. – reference: Ziegler, C., Bremer, E., and Krämer, R. (2010) The BCCT family of carriers: from physiology to crystal structure. Mol Microbiol 78: 13-34. – reference: Pedruzzi, I., Rivoire, C., Auchincloss, A.H., Coudert, E., Keller, G., de Castro, E., et al. (2015) HAMAP in 2015: updates to the protein family classification and annotation system. Nucleic Acids Res 43: D1064-D1070. – reference: Nogales, J., Canales, A., Jiménez-Barbero, J., García, J.L., and Díaz, E. (2005) Molecular characterization of the gallate dioxygenase from Pseudomonas putida KT2440. The prototype of a new subgroup of extradiol dioxygenases. J Biol Chem 280: 35382-35390. – reference: Sudom, A., Walters, R., Pastushok, L., Goldie, D., Prasad, L., Delbaere, L.T.J., and Goldie, H. (2003) Mechanisms of activation of phosphoenolpyruvate carboxykinase from Escherichia coli by Ca2+ and of desensitization by trypsin. J Bacteriol 185: 4233-4242. – reference: Puchałka, J., Oberhardt, M.A., Godinho, M., Bielecka, A., Regenhardt, D., Timmis, K.N., et al. (2008) Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Comput Biol 4: e1000210. – reference: Sohn, S.B., Kim, T.Y., Park, J.M., and Lee, S.Y. (2010) In silico genome-scale metabolic analysis of Pseudomonas putida KT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival. Biotechnol J 5: 739-750. – reference: Nogales, J., Palsson, B.Ø., and Thiele, I. (2008) A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol 2: 79. – reference: Dover, N., and Padan, E. (2001) Transcription of nhaA, the main Na+/H+ antiporter of Escherichia coli, is regulated by Na+ and growth phase. J Bacteriol 183: 644-653. – reference: Yu, N.Y., Laird, M.R., Spencer, C., and Brinkman, F.S.L. (2011) PSORTdb-an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea. Nucleic Acids Res 39: D241-D244. – reference: Nikel, P.I., Martínez-García, E., and de Lorenzo, V. (2014) Biotechnological domestication of pseudomonads using synthetic biology. Nat Rev Microbiol 12: 368-379. – reference: MacMillan, S.V., Alexander, D.A., Culham, D.E., Kunte, H.J., Marshall, E.V., Rochon, D., and Wood, J.M. (1999) The ion coupling and organic substrate specificities of osmoregulatory transporter ProP in Escherichia coli. Biochim Biophys Acta 1420: 30-44. – reference: Yang, L., Tan, J., O'Brien, E.J., Monk, J.M., Kim, D., Li, H.J., et al. (2015) Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proc Natl Acad Sci 112: 201501384. – reference: Mitchell, A., Chang, H.-Y., Daugherty, L., Fraser, M., Hunter, S., Lopez, R., et al. (2015) The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res 43: D213-D221. – reference: Smith, T.F., and Waterman, M.S. (1981) Identification of common molecular subsequences. J Mol Biol 147: 195-197. – reference: Rahav-Manor, O., Carmel, O., Karpel, R., Taglicht, D., Glaser, G., Schuldiner, S., and Padan, E. (1992) NhaR, a protein homologous to a family of bacterial regulatory proteins (LysR), regulates nhaA, the sodium proton antiporter gene in Escherichia coli. J Biol Chem 267: 10433-10438. – reference: Chen, C., Malek, A.A., Wargo, M.J., Hogan, D.A., and Beattie, G.A. (2010) The ATP-binding cassette transporter Cbc (choline/betaine/carnitine) recruits multiple substrate-binding proteins with strong specificity for distinct quaternary ammonium compounds. Mol Microbiol 75: 29-45. – reference: Overhage, J., Priefert, H., and Steinbüchel, A. (1999) Biochemical and genetic analyses of ferulic acid catabolism in Pseudomonas sp. strain HR199. Appl Environ Microbiol 65: 4837-4847. – reference: Acevedo-Rocha, C.G., Fang, G., Schmidt, M., Ussery, D.W., and Danchin, A. (2013) From essential to persistent genes: a functional approach to constructing synthetic life. Trends Genet 29: 273-279. – reference: The UniProt Consortium (2014) UniProt: a hub for protein information. Nucleic Acids Res 43: D204-D212. – reference: Lewinson, O., Padan, E., and Bibi, E. (2004) Alkalitolerance: a biological function for a multidrug transporter in pH homeostasis. Proc Natl Acad Sci U S A 101: 14073-14078. – reference: Ye, L., Hildebrand, F., Dingemans, J., Ballet, S., Laus, G., Matthijs, S., et al. (2014) Draft genome sequence analysis of a Pseudomonas putida W15Oct28 strain with antagonistic activity to Gram-positive and Pseudomonas sp. pathogens. PLoS One 9: e110038. – reference: Danchin, A., and Sekowska, A. (2014) The logic of metabolism and its fuzzy consequences. Environ Microbiol 16: 19-28. – reference: Saparov, S.M., Antonenko, Y.N., and Pohl, P. (2006) A new model of weak acid permeation through membranes revisited: does Overton still rule? Biophys J 90: L86-L88. – reference: Stancik, L.M., Stancik, D.M., Schmidt, B., Barnhart, D.M., Yoncheva, Y.N., and Slonczewski, J.L. (2002) pH-dependent expression of periplasmic proteins and amino acid catabolism in Escherichia coli. J Bacteriol 184: 4246-4258. – reference: Kumar, V.S., and Maranas, C.D. (2009) GrowMatch: an automated method for reconciling in silico/in vivo growth predictions. PLoS Comput Biol 5: e1000308. – reference: Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079. – reference: Elbein, A.D., Pastuszak, I., Tackett, A.J., Wilson, T., and Pan, Y.T. (2010) Last step in the conversion of trehalose to glycogen: a mycobacterial enzyme that transfers maltose from maltose 1-phosphate to glycogen. J Biol Chem 285: 9803-9812. – reference: Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E.L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567-580. – reference: Lund, P., Tramonti, A., and De Biase, D. (2014) Coping with low pH: molecular strategies in neutralophilic bacteria. FEMS Microbiol Rev 38: 1091-1125. – reference: Barrick, J.E., Yu, D.S., Yoon, S.H., Jeong, H., Oh, T.K., Schneider, D., et al. (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461: 1243-1247. – reference: Golovan, S., Wang, G., Zhang, J., and Forsberg, C.W. (2000) Characterization and overproduction of the Escherichia coli appA encoded bifunctional enzyme that exhibits both phytase and acid phosphatase activities. Can J Microbiol 46: 59-71. – reference: Morgat, A., Axelsen, K.B., Lombardot, T., Alcántara, R., Aimo, L., Zerara, M., et al. (2015) Updates in Rhea-a manually curated resource of biochemical reactions. Nucleic Acids Res 43: D459-D464. – reference: Ramazzina, I., Folli, C., Secchi, A., Berni, R., and Percudani, R. (2006) Completing the uric acid degradation pathway through phylogenetic comparison of whole genomes. Nat Chem Biol 2: 144-148. – reference: Burge, S.W., Daub, J., Eberhardt, R., Tate, J., Barquist, L., Nawrocki, E.P., et al. (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Res 41: D226-D232. – reference: Chang, A., Schomburg, I., Placzek, S., Jeske, L., Ulbrich, M., Xiao, M., et al. (2015) BRENDA in 2015: exciting developments in its 25th year of existence. Nucleic Acids Res 43: D439-D446. – reference: La Rosa, R., Nogales, J., and Rojo, F. (2015) The Crc/CrcZ-CrcY global regulatory system helps the integration of gluconeogenic and glycolytic metabolism in Pseudomonas putida. Environ Microbiol 17: 3362-3378. – reference: Nelson, K.E., Weinel, C., Paulsen, I.T., Dodson, R.J., Hilbert, H., Martins dos Santos, V. A. P., et al. (2002) Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4: 799-808. – reference: Timinskas, K., Balvočiūtė, M., Timinskas, A., and Venclovas, Č. (2014) Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes. Nucleic Acids Res 42: 1393-1413. – reference: Akashi, H., and Gojobori, T. (2002) Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci U S A 99: 3695-3700. – reference: Foster, J.W. (1999) When protons attack: microbial strategies of acid adaptation. Curr Opin Microbiol 2: 170-174. – reference: Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C.A., et al. (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 42: D459-D471. – reference: Carmel, O., Rahav-Manor, O., Dover, N., Shaanan, B., and Padan, E. (1997) The Na+-specific interaction between the LysR-type regulator, NhaR, and the nhaA gene encoding the Na+/H+ antiporter of Escherichia coli. EMBO J 16: 5922-5929. – reference: Chen, C., and Beattie, G.A. (2008) Pseudomonas syringae BetT is a low-affinity choline transporter that is responsible for superior osmoprotection by choline over glycine betaine. J Bacteriol 190: 2717-2725. – reference: Kim, Y.H., Cho, K., Yun, S.-H., Kim, J.Y., Kwon, K.-H., Yoo, J.S., and Kim, S.I. (2006) Analysis of aromatic catabolic pathways in Pseudomonas putida KT2440 using a combined proteomic approach: 2-DE/MS and cleavable isotope-coded affinity tag analysis. Proteomics 6: 1301-1318. – reference: Kobayashi, K., Kato, M., Miura, Y., Kettoku, M., Komeda, T., and Iwamatsu, A. (1996) Gene analysis of trehalose-producing enzymes from hyperthermophilic archaea in Sulfolobales. Biosci Biotechnol Biochem 60: 1720-1723. – reference: Bay, D.C., and Turner, R.J. (2012) Small multidrug resistance protein EmrE reduces host pH and osmotic tolerance to metabolic quaternary cation osmoprotectants. J Bacteriol 194: 5941-5948. – reference: Osterman, A. (2006) A hidden metabolic pathway exposed. Proc Natl Acad Sci U S A 103: 5637-5638. – reference: Leprince, A., Janus, D., de Lorenzo, V., and dos Santos, V.M. (2012) Streamlining of a Pseudomonas putida genome using a combinatorial deletion method based on minitransposon insertion and the Flp-FRT recombination system. Methods Mol Biol 813: 249-266. – reference: Galperin, M.Y., Makarova, K.S., Wolf, Y.I., and Koonin, E. V (2015) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 43: D261-D269. – reference: Smith, L.T., Pocard, J.A., Bernard, T., and Le Rudulier, D. (1988) Osmotic control of glycine betaine biosynthesis and degradation in Rhizobium meliloti. J Bacteriol 170: 3142-3149. – reference: Parschat, K., Canne, C., Hüttermann, J., Kappl, R., and Fetzner, S. (2001) Xanthine dehydrogenase from Pseudomonas putida 86: specificity, oxidation-reduction potentials of its redox-active centers, and first EPR characterization. Biochim Biophys Acta 1544: 151-165. – reference: Lawrence, M., Huber, W., Pagès, H., Aboyoun, P., Carlson, M., Gentleman, R., et al. (2013) Software for computing and annotating genomic ranges. PLoS Comput Biol 9: e1003118. – reference: Molina-Henares, M.A., de la Torre, J., García-Salamanca, A., Molina-Henares, A.J., Herrera, M.C., Ramos, J.L., and Duque, E. (2010) Identification of conditionally essential genes for growth of Pseudomonas putida KT2440 on minimal medium through the screening of a genome-wide mutant library. Environ Microbiol 12: 1468-1485. – reference: Hidese, R., Mihara, H., Kurihara, T., and Esaki, N. (2011) Escherichia coli dihydropyrimidine dehydrogenase is a novel NAD-dependent heterotetramer essential for the production of 5,6-dihydrouracil. J Bacteriol 193: 989-993. – reference: Ramos-González, M.I., and Molin, S. (1998) Cloning, sequencing, and phenotypic characterization of the rpoS gene from Pseudomonas putida KT2440. J Bacteriol 180: 3421-3431. – reference: Hastings, J., de Matos, P., Dekker, A., Ennis, M., Harsha, B., Kale, N., et al. (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res 41: D456-D463. – reference: Mikoulinskaia, G.V., Zimin, A.A., Feofanov, S.A., and Miroshnikov, A.I. (2004) Identification, cloning, and expression of bacteriophage T5 dnk gene encoding a broad specificity deoxyribonucleoside monophosphate kinase (EC 2.7.4.13). Protein Expr Purif 33: 166-175. – reference: Wargo, M.J., Szwergold, B.S., and Hogan, D.A. (2008) Identification of two gene clusters and a transcriptional regulator required for Pseudomonas aeruginosa glycine betaine catabolism. J Bacteriol 190: 2690-2699. – reference: Hyatt, D., Chen, G.-L., Locascio, P.F., Land, M.L., Larimer, F.W., and Hauser, L.J. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119. – reference: West, T.P. (2001) Pyrimidine base catabolism in Pseudomonas putida biotype B. Antonie van Leeuwenhoek 80: 163-167. – reference: Bochner, B.R. (1989) Sleuthing out bacterial identities. Nature 339: 157-158. – reference: Milanesio, P., Arce-Rodríguez, A., Muñoz, A., Calles, B., and de Lorenzo, V. (2011) Regulatory exaptation of the catabolite repression protein (Crp)-cAMP system in Pseudomonas putida. Environ Microbiol 13: 324-339. – reference: Bocs, S., Cruveiller, S., Vallenet, D., Nuel, G., and Médigue, C. (2003) AMIGene: annotation of MIcrobial Genes. Nucleic Acids Res 31: 3723-3726. – reference: Gralla, J.D., and Vargas, D.R. (2006) Potassium glutamate as a transcriptional inhibitor during bacterial osmoregulation. EMBO J 25: 1515-1521. – reference: Brett, C.L., Donowitz, M., and Rao, R. (2005) Evolutionary origins of eukaryotic sodium/proton exchangers. Am J Physiol Cell Physiol 288: C223-C239. – reference: Bernard, T., Bridge, A., Morgat, A., Moretti, S., Xenarios, I., and Pagni, M. (2014) Reconciliation of metabolites and biochemical reactions for metabolic networks. Brief Bioinform 15: 123-135. – reference: De Smet, K.A., Weston, A., Brown, I.N., Young, D.B., and Robertson, B.D. (2000) Three pathways for trehalose biosynthesis in mycobacteria. Microbiology 146: 199-208. – reference: Dos Santos, V.A.P.M., Heim, S., Moore, E.R.B., Strätz, M., and Timmis, K.N. (2004) Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ Microbiol 6: 1264-1286. – reference: Achaz, G., Coissac, E., Viari, A., and Netter, P. (2000) Analysis of intrachromosomal duplications in yeast Saccharomyces cerevisiae: a possible model for their origin. Mol Biol Evol 17: 1268-1275. – reference: Bochner, B.R., Gadzinski, P., and Panomitros, E. (2001) Phenotype microarrays for high-throughput phenotypic testing and assay of gene function. Genome Res 11: 1246-1255. – reference: Gassel, M., Möllenkamp, T., Puppe, W., and Altendorf, K. (1999) The KdpF subunit is part of the K+-translocating Kdp complex of Escherichia coli and is responsible for stabilization of the complex in vitro. J Biol Chem 274: 37901-37907. – reference: Udaondo, Z., Molina, L., Segura, A., Duque, E., and Ramos, J.L. (2015) Analysis of the core genome and pangenome of Pseudomonas putida. Environ Microbiol, In press, DOI: 10.1111/1462-2920.13015. – reference: Wargo, M.J. (2013) Homeostasis and catabolism of choline and glycine betaine: lessons from Pseudomonas aeruginosa. Appl Environ Microbiol 79: 2112-2120. – reference: Engelen, S., Vallenet, D., Médigue, C., and Danchin, A. (2012) Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC. BMC Genom 13: 69. – reference: Touchon, M., Hoede, C., Tenaillon, O., Barbe, V., Baeriswyl, S., Bidet, P., et al. (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5: e1000344. – reference: Winsor, G.L., Lam, D.K.W., Fleming, L., Lo, R., Whiteside, M.D., Yu, N.Y., et al. (2011) Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res 39: D596-D600. – reference: Demerec, M., Adelberg, E.A., Clark, A.J., and Hartman, P.E. (1966) A proposal for a uniform nomenclature in bacterial genetics. Genetics 54: 61-76. – reference: Velasco-García, R., Villalobos, M.A., Ramírez-Romero, M.A., Mújica-Jiménez, C., Iturriaga, G., and Muñoz-Clares, R.A. (2006) Betaine aldehyde dehydrogenase from Pseudomonas aeruginosa: cloning, over-expression in Escherichia coli, and regulation by choline and salt. Arch Microbiol 185: 14-22. – reference: Smith, A.A.T., Belda, E., Viari, A., Medigue, C., and Vallenet, D. (2012) The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes. PLoS Comput Biol 8: e1002540. – reference: Pinner, E., Kotler, Y., Padan, E., and Schuldiner, S. (1993) Physiological role of nhaB, a specific Na+/H+ antiporter in Escherichia coli. J Biol Chem 268: 1729-1734. – reference: Foster, J.W. (2004) Escherichia coli acid resistance: tales of an amateur acidophile. Nat Rev Microbiol 2: 898-907. – reference: Ganter, M., Bernard, T., Moretti, S., Stelling, J., and Pagni, M. (2013) MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks. Bioinformatics 29: 815-816. – reference: Heavner, B.D., Smallbone, K., Price, N.D., and Walker, L.P. (2013) Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance. Database (Oxford) 2013: bat059. – reference: Chandra, G., Chater, K.F., and Bornemann, S. (2011) Unexpected and widespread connections between bacterial glycogen and trehalose metabolism. Microbiology 157: 1565-1572. – reference: Barrett, T., Wilhite, S.E., Ledoux, P., Evangelista, C., Kim, I.F., Tomashevsky, M., et al. (2013) NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res 41: D991-D995. – reference: Lowe, T.M., and Eddy, S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964. – reference: Scovill, W.H., Schreier, H.J., and Bayles, K.W. (1996) Identification and characterization of the pckA gene from Staphylococcus aureus. J Bacteriol 178: 3362-3364. – reference: Frank, S., Klockgether, J., Hagendorf, P., Geffers, R., Schöck, U., Pohl, T., et al. (2011) Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray transcriptomics. Environ Microbiol 13: 1309-1326. – reference: Padan, E., Bibi, E., Ito, M., and Krulwich, T.A. (2005) Alkaline pH homeostasis in bacteria: new insights. Biochim Biophys Acta 1717: 67-88. – reference: Bettenbrock, K., Bai, H., Ederer, M., Green, J., Hellingwerf, K.J., Holcombe, M., et al. (2014) Towards a systems level understanding of the oxygen response of Escherichia coli. Adv Microb Physiol 64: 65-114. – reference: Kajiyama, Y., Otagiri, M., Sekiguchi, J., Kosono, S., and Kudo, T. (2007) Complex formation by the mrpABCDEFG gene products, which constitute a principal Na+/H+ antiporter in Bacillus subtilis. J Bacteriol 189: 7511-7514. – reference: Meyer, F., Overbeek, R., and Rodriguez, A. (2009) FIGfams: yet another set of protein families. Nucleic Acids Res 37: 6643-6654. – reference: Reynes, J.P., Tiraby, M., Baron, M., Drocourt, D., and Tiraby, G. (1996) Escherichia coli thymidylate kinase: molecular cloning, nucleotide sequence, and genetic organization of the corresponding tmk locus. J Bacteriol 178: 2804-2812. – reference: Chien, H.R., Jih, Y.L., Yang, W.Y., and Hsu, W.H. (1998) Identification of the open reading frame for the Pseudomonas putida D-hydantoinase gene and expression of the gene in Escherichia coli. Biochim Biophys Acta 1395: 68-77. – reference: Oberhardt, M.A., Puchałka, J., Martins dos Santos, V.A.P., and Papin, J.A. (2011) Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis. PLoS Comput Biol 7: e1001116. – reference: Hui, S., Silverman, J.M., Chen, S.S., Erickson, D.W., Basan, M., Wang, J., et al. (2015) Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria. Mol Syst Biol 11: e784. – reference: Regenhardt, D., Heuer, H., Heim, S., Fernandez, D.U., Strömpl, C., Moore, E.R.B., and Timmis, K.N. (2002) Pedigree and taxonomic credentials of Pseudomonas putida strain KT2440. Environ Microbiol 4: 912-915. – volume: 25 start-page: 2078 year: 2009 end-page: 2079 article-title: The Sequence Alignment/Map format and SAMtools publication-title: Bioinformatics – volume: 6 start-page: 1264 year: 2004 end-page: 1286 article-title: Insights into the genomic basis of niche specificity of KT2440 publication-title: Environ Microbiol – volume: 193 start-page: 989 year: 2011 end-page: 993 article-title: dihydropyrimidine dehydrogenase is a novel NAD‐dependent heterotetramer essential for the production of 5,6‐dihydrouracil publication-title: J Bacteriol – volume: 11 start-page: 1725 year: 2001 end-page: 1729 article-title: SSAHA: a fast search method for large DNA databases publication-title: Genome Res – volume: 103 start-page: 5637 year: 2006 end-page: 5638 article-title: A hidden metabolic pathway exposed publication-title: Proc Natl Acad Sci U S A – volume: 54 start-page: 61 year: 1966 end-page: 76 article-title: A proposal for a uniform nomenclature in bacterial genetics publication-title: Genetics – volume: 39 start-page: D241 year: 2011 end-page: D244 article-title: PSORTdb–an expanded, auto‐updated, user‐friendly protein subcellular localization database for Bacteria and Archaea publication-title: Nucleic Acids Res – volume: 112 start-page: 201501384 year: 2015 article-title: Systems biology definition of the core proteome of metabolism and expression is consistent with high‐throughput data publication-title: Proc Natl Acad Sci – volume: 16 start-page: 19 year: 2014 end-page: 28 article-title: The logic of metabolism and its fuzzy consequences publication-title: Environ Microbiol – volume: 283 start-page: 23295 year: 2008 end-page: 23304 article-title: Logical identification of an allantoinase analog ( ) recruited from polysaccharide deacetylases publication-title: J Biol Chem – volume: 5 start-page: e1000344 year: 2009 article-title: Organised genome dynamics in the species results in highly diverse adaptive paths publication-title: PLoS Genet – volume: 189 start-page: 7511 year: 2007 end-page: 7514 article-title: Complex formation by the gene products, which constitute a principal Na /H antiporter in publication-title: J Bacteriol – volume: 1717 start-page: 67 year: 2005 end-page: 88 article-title: Alkaline pH homeostasis in bacteria: new insights publication-title: Biochim Biophys Acta – volume: 183 start-page: 644 year: 2001 end-page: 653 article-title: Transcription of , the main Na /H antiporter of , is regulated by Na and growth phase publication-title: J Bacteriol – volume: 2 start-page: 79 year: 2008 article-title: A genome‐scale metabolic reconstruction of KT2440: JN746 as a cell factory publication-title: BMC Syst Biol – volume: 17 start-page: 3362 year: 2015 end-page: 3378 article-title: The Crc/CrcZ‐CrcY global regulatory system helps the integration of gluconeogenic and glycolytic metabolism in publication-title: Environ Microbiol – volume: 267 start-page: 10433 year: 1992 end-page: 10438 article-title: NhaR, a protein homologous to a family of bacterial regulatory proteins (LysR), regulates , the sodium proton antiporter gene in publication-title: J Biol Chem – volume: 39 start-page: D596 year: 2011 end-page: D600 article-title: Genome Database: improved comparative analysis and population genomics capability for genomes publication-title: Nucleic Acids Res – volume: 13 start-page: 69 year: 2012 article-title: Distinct co‐evolution patterns of genes associated to DNA polymerase III DnaE and PolC publication-title: BMC Genom – volume: 178 start-page: 2804 year: 1996 end-page: 2812 article-title: thymidylate kinase: molecular cloning, nucleotide sequence, and genetic organization of the corresponding locus publication-title: J Bacteriol – volume: 49 start-page: 1 year: 2003 end-page: 9 article-title: Control of transcription in and : why so different? publication-title: Mol Microbiol – volume: 41 start-page: D605 year: 2013 end-page: D612 article-title: EcoCyc: fusing model organism databases with systems biology publication-title: Nucleic Acids Res – volume: 80 start-page: 163 year: 2001 end-page: 167 article-title: Pyrimidine base catabolism in biotype B publication-title: Antonie van Leeuwenhoek – volume: 5 start-page: e1000308 year: 2009 article-title: GrowMatch: an automated method for reconciling in silico/in vivo growth predictions publication-title: PLoS Comput Biol – volume: 1784 start-page: 431 year: 2008 end-page: 444 article-title: Amidohydrolases of the reductive pyrimidine catabolic pathway purification, characterization, structure, reaction mechanisms and enzyme deficiency publication-title: Biochim Biophys Acta – volume: 274 start-page: 37901 year: 1999 end-page: 37907 article-title: The KdpF subunit is part of the K ‐translocating Kdp complex of and is responsible for stabilization of the complex publication-title: J Biol Chem – volume: 157 start-page: 1565 year: 2011 end-page: 1572 article-title: Unexpected and widespread connections between bacterial glycogen and trehalose metabolism publication-title: Microbiology – volume: 190 start-page: 2717 year: 2008 end-page: 2725 article-title: BetT is a low‐affinity choline transporter that is responsible for superior osmoprotection by choline over glycine betaine publication-title: J Bacteriol – volume: 178 start-page: 1663 year: 1996 end-page: 1670 article-title: DNA‐binding properties of the BetI repressor protein of : the inducer choline stimulates BetI‐DNA complex formation publication-title: J Bacteriol – volume: 285 start-page: 9803 year: 2010 end-page: 9812 article-title: Last step in the conversion of trehalose to glycogen: a mycobacterial enzyme that transfers maltose from maltose 1‐phosphate to glycogen publication-title: J Biol Chem – volume: 8 start-page: 785 year: 2011 end-page: 786 article-title: SignalP 4.0: discriminating signal peptides from transmembrane regions publication-title: Nat Methods – volume: 12 start-page: 1468 year: 2010 end-page: 1485 article-title: Identification of conditionally essential genes for growth of KT2440 on minimal medium through the screening of a genome‐wide mutant library publication-title: Environ Microbiol – volume: 101 start-page: 14073 year: 2004 end-page: 14078 article-title: Alkalitolerance: a biological function for a multidrug transporter in pH homeostasis publication-title: Proc Natl Acad Sci U S A – volume: 64 start-page: 65 year: 2014 end-page: 114 article-title: Towards a systems level understanding of the oxygen response of publication-title: Adv Microb Physiol – volume: 147 start-page: 195 year: 1981 end-page: 197 article-title: Identification of common molecular subsequences publication-title: J Mol Biol – volume: 4 start-page: 912 year: 2002 end-page: 915 article-title: Pedigree and taxonomic credentials of strain KT2440 publication-title: Environ Microbiol – volume: 13 start-page: 324 year: 2011 end-page: 339 article-title: Regulatory exaptation of the catabolite repression protein (Crp)‐cAMP system in publication-title: Environ Microbiol – volume: 5 start-page: 883 year: 2013 end-page: 891 article-title: Transcriptomic fingerprinting of under alternative physiological regimes publication-title: Environ Microbiol Rep – volume: 13 start-page: 1309 year: 2011 end-page: 1326 article-title: KT2440 genome update by cDNA sequencing and microarray transcriptomics publication-title: Environ Microbiol – volume: 290 start-page: 25920 year: 2015 end-page: 25932 article-title: KT2440 strain metabolizes glucose through a cycle formed by enzymes of the Entner‐Doudoroff, Embden‐Meyerhof‐Parnas, and pentose phosphate pathways publication-title: J Biol Chem – volume: 31 start-page: 6633 year: 2003 end-page: 6639 article-title: Enzyme‐specific profiles for genome annotation: PRIAM publication-title: Nucleic Acids Res – volume: 38 start-page: 1091 year: 2014 end-page: 1125 article-title: Coping with low pH: molecular strategies in neutralophilic bacteria publication-title: FEMS Microbiol Rev – volume: 5 start-page: 739 year: 2010 end-page: 750 article-title: genome‐scale metabolic analysis of KT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival publication-title: Biotechnol J – volume: 41 start-page: D991 year: 2013 end-page: D995 article-title: NCBI GEO: archive for functional genomics data sets–update publication-title: Nucleic Acids Res – volume: 43 start-page: D204 year: 2014 end-page: D212 article-title: UniProt: a hub for protein information publication-title: Nucleic Acids Res – volume: 43 start-page: D213 year: 2015 end-page: D221 article-title: The InterPro protein families database: the classification resource after 15 years publication-title: Nucleic Acids Res – volume: 32 start-page: 559 year: 2007 end-page: 568 article-title: The Kdp‐ATPase system and its regulation publication-title: J Biosci – volume: 25 start-page: 1515 year: 2006 end-page: 1521 article-title: Potassium glutamate as a transcriptional inhibitor during bacterial osmoregulation publication-title: EMBO J – volume: 280 start-page: 35382 year: 2005 end-page: 35390 article-title: Molecular characterization of the gallate dioxygenase from KT2440. The prototype of a new subgroup of extradiol dioxygenases publication-title: J Biol Chem – volume: 35 start-page: 652 year: 2011 end-page: 680 article-title: genomes: diverse and adaptable publication-title: FEMS Microbiol Rev – volume: 2013 start-page: bat059 year: 2013 article-title: Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance publication-title: Database (Oxford) – volume: 68 start-page: 213 year: 2005 end-page: 219 article-title: Cloning and expression of a trehalose synthase from CJ38 in for the production of trehalose publication-title: Appl Microbiol Biotechnol – volume: 155 start-page: 2411 year: 2009 end-page: 2419 article-title: Identification of genes required for carnitine catabolism publication-title: Microbiology – volume: 1395 start-page: 68 year: 1998 end-page: 77 article-title: Identification of the open reading frame for the D‐hydantoinase gene and expression of the gene in publication-title: Biochim Biophys Acta – volume: 7 start-page: 18 year: 2015 end-page: 19 article-title: It's the metabolism, stupid! publication-title: Environ Microbiol Rep – volume: 172 start-page: 4339 year: 1990 end-page: 4347 article-title: , an gene essential for survival in stationary phase publication-title: J Bacteriol – volume: 7 start-page: e1001116 year: 2011 article-title: Reconciliation of genome‐scale metabolic reconstructions for comparative systems analysis publication-title: PLoS Comput Biol – volume: 12 start-page: 368 year: 2014 end-page: 379 article-title: Biotechnological domestication of pseudomonads using synthetic biology publication-title: Nat Rev Microbiol – volume: 6 start-page: 1301 year: 2006 end-page: 1318 article-title: Analysis of aromatic catabolic pathways in KT2440 using a combined proteomic approach: 2‐DE/MS and cleavable isotope‐coded affinity tag analysis publication-title: Proteomics – volume: 37 start-page: 6643 year: 2009 end-page: 6654 article-title: FIGfams: yet another set of protein families publication-title: Nucleic Acids Res – volume: 813 start-page: 249 year: 2012 end-page: 266 article-title: Streamlining of a genome using a combinatorial deletion method based on minitransposon insertion and the Flp‐FRT recombination system publication-title: Methods Mol Biol – volume: 16 start-page: 5922 year: 1997 end-page: 5929 article-title: The Na ‐specific interaction between the LysR‐type regulator, NhaR, and the gene encoding the Na /H antiporter of publication-title: EMBO J – volume: 105 start-page: 11329 year: 2008 end-page: 11334 article-title: Deciphering the genetic determinants for aerobic nicotinic acid degradation: the cluster from KT2440 publication-title: Proc Natl Acad Sci U S A – volume: 25 start-page: 955 year: 1997 end-page: 964 article-title: tRNAscan‐SE: a program for improved detection of transfer RNA genes in genomic sequence publication-title: Nucleic Acids Res – volume: 11 start-page: 119 year: 2010 article-title: Prodigal: prokaryotic gene recognition and translation initiation site identification publication-title: BMC Bioinformatics – volume: 4 start-page: 799 year: 2002 end-page: 808 article-title: Complete genome sequence and comparative analysis of the metabolically versatile KT2440 publication-title: Environ Microbiol – volume: 15 start-page: 123 year: 2014 end-page: 135 article-title: Reconciliation of metabolites and biochemical reactions for metabolic networks publication-title: Brief Bioinform – volume: 31 start-page: 3723 year: 2003 end-page: 3726 article-title: AMIGene: annotation of MIcrobial Genes publication-title: Nucleic Acids Res – volume: 4 start-page: e1000210 year: 2008 article-title: Genome‐scale reconstruction and analysis of the KT2440 metabolic network facilitates applications in biotechnology publication-title: PLoS Comput Biol – volume: 6 start-page: 1290 year: 2011 end-page: 1307 article-title: Quantitative prediction of cellular metabolism with constraint‐based models: the COBRA Toolbox v2.0 publication-title: Nat Protoc – volume: 99 start-page: 3695 year: 2002 end-page: 3700 article-title: Metabolic efficiency and amino acid composition in the proteomes of and publication-title: Proc Natl Acad Sci U S A – volume: 11 start-page: R106 year: 2010 article-title: Differential expression analysis for sequence count data publication-title: Genome Biol – volume: 42 start-page: D459 year: 2014 end-page: D471 article-title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases publication-title: Nucleic Acids Res – volume: 65 start-page: 4837 year: 1999 end-page: 4847 article-title: Biochemical and genetic analyses of ferulic acid catabolism in sp. strain HR199 publication-title: Appl Environ Microbiol – volume: 29 start-page: 273 year: 2013 end-page: 279 article-title: From essential to persistent genes: a functional approach to constructing synthetic life publication-title: Trends Genet – volume: 9 start-page: e1003118 year: 2013 article-title: Software for computing and annotating genomic ranges publication-title: PLoS Comput Biol – volume: 461 start-page: 1243 year: 2009 end-page: 1247 article-title: Genome evolution and adaptation in a long‐term experiment with publication-title: Nature – volume: 174 start-page: 889 year: 1992 end-page: 898 article-title: Molecular cloning and physical mapping of the genes, which encode the osmoregulatory trehalose pathway of : evidence that transcription is activated by (AppR) publication-title: J Bacteriol – volume: 2 start-page: 898 year: 2004 end-page: 907 article-title: acid resistance: tales of an amateur acidophile publication-title: Nat Rev Microbiol – volume: 185 start-page: 14 year: 2006 end-page: 22 article-title: Betaine aldehyde dehydrogenase from : cloning, over‐expression in , and regulation by choline and salt publication-title: Arch Microbiol – volume: 17 start-page: 1268 year: 2000 end-page: 1275 article-title: Analysis of intrachromosomal duplications in yeast : a possible model for their origin publication-title: Mol Biol Evol – volume: 43 start-page: D1064 year: 2015 end-page: D1070 article-title: HAMAP in 2015: updates to the protein family classification and annotation system publication-title: Nucleic Acids Res – volume: 178 start-page: 3362 year: 1996 end-page: 3364 article-title: Identification and characterization of the gene from publication-title: J Bacteriol – volume: 41 start-page: D636 year: 2013 end-page: D647 article-title: MicroScope–an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data publication-title: Nucleic Acids Res – year: 2015 article-title: Analysis of the core genome and pangenome of publication-title: Environ Microbiol – volume: 42 start-page: 1393 year: 2014 end-page: 1413 article-title: Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes publication-title: Nucleic Acids Res – volume: 29 start-page: 815 year: 2013 end-page: 816 article-title: MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks publication-title: Bioinformatics – volume: 4 start-page: 824 year: 2002 end-page: 841 article-title: Genomic analysis of the aromatic catabolic pathways from KT2440 publication-title: Environ Microbiol – volume: 35 start-page: 299 year: 2011 end-page: 323 article-title: Comparative genomics and functional analysis of niche‐specific adaptation in publication-title: FEMS Microbiol Rev – volume: 2 start-page: 170 year: 1999 end-page: 174 article-title: When protons attack: microbial strategies of acid adaptation publication-title: Curr Opin Microbiol – volume: 79 start-page: 2112 year: 2013 end-page: 2120 article-title: Homeostasis and catabolism of choline and glycine betaine: lessons from publication-title: Appl Environ Microbiol – volume: 35 start-page: 3100 year: 2007 end-page: 3108 article-title: RNAmmer: consistent and rapid annotation of ribosomal RNA genes publication-title: Nucleic Acids Res – volume: 268 start-page: 1729 year: 1993 end-page: 1734 article-title: Physiological role of , a specific Na /H antiporter in publication-title: J Biol Chem – volume: 90 start-page: L86 year: 2006 end-page: L88 article-title: A new model of weak acid permeation through membranes revisited: does Overton still rule? publication-title: Biophys J – volume: 13 start-page: 93 year: 2013 article-title: Reconciling in vivo and in silico key biological parameters of KT2440 during growth on glucose under carbon‐limited condition publication-title: BMC Biotechnol – volume: 33 start-page: 166 year: 2004 end-page: 175 article-title: Identification, cloning, and expression of bacteriophage T5 gene encoding a broad specificity deoxyribonucleoside monophosphate kinase (EC 2.7.4.13) publication-title: Protein Expr Purif – volume: 41 start-page: D226 year: 2013 end-page: D232 article-title: Rfam 11.0: 10 years of RNA families publication-title: Nucleic Acids Res – volume: 305 start-page: 567 year: 2001 end-page: 580 article-title: Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes publication-title: J Mol Biol – volume: 1544 start-page: 151 year: 2001 end-page: 165 article-title: Xanthine dehydrogenase from 86: specificity, oxidation‐reduction potentials of its redox‐active centers, and first EPR characterization publication-title: Biochim Biophys Acta – volume: 170 start-page: 3142 year: 1988 end-page: 3149 article-title: Osmotic control of glycine betaine biosynthesis and degradation in publication-title: J Bacteriol – volume: 194 start-page: 5941 year: 2012 end-page: 5948 article-title: Small multidrug resistance protein EmrE reduces host pH and osmotic tolerance to metabolic quaternary cation osmoprotectants publication-title: J Bacteriol – volume: 1 start-page: 141 year: 1984 end-page: 199 – volume: 11 start-page: e784 year: 2015 article-title: Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria publication-title: Mol Syst Biol – volume: 41 start-page: D456 year: 2013 end-page: D463 article-title: The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013 publication-title: Nucleic Acids Res – volume: 10 start-page: 413 year: 2008 end-page: 432 article-title: Genetic analyses and molecular characterization of the pathways involved in the conversion of 2‐phenylethylamine and 2‐phenylethanol into phenylacetic acid in U publication-title: Environ Microbiol – volume: 288 start-page: C223 year: 2005 end-page: C239 article-title: Evolutionary origins of eukaryotic sodium/proton exchangers publication-title: Am J Physiol Cell Physiol – volume: 10 start-page: 42 year: 2014 end-page: 49 article-title: Revealing the hidden functional diversity of an enzyme family publication-title: Nat Chem Biol – volume: 75 start-page: 29 year: 2010 end-page: 45 article-title: The ATP‐binding cassette transporter Cbc (choline/betaine/carnitine) recruits multiple substrate‐binding proteins with strong specificity for distinct quaternary ammonium compounds publication-title: Mol Microbiol – volume: 5 start-page: 424 year: 2011 end-page: 429 article-title: The pathway tools pathway prediction algorithm publication-title: Stand Genom Sci – volume: 8 start-page: e1002540 year: 2012 article-title: The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes publication-title: PLoS Comput Biol – volume: 1420 start-page: 30 year: 1999 end-page: 44 article-title: The ion coupling and organic substrate specificities of osmoregulatory transporter ProP in publication-title: Biochim Biophys Acta – volume: 79 start-page: 359 year: 2011 end-page: 374 article-title: Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from publication-title: Mol Microbiol – volume: 60 start-page: 1720 year: 1996 end-page: 1723 article-title: Gene analysis of trehalose‐producing enzymes from hyperthermophilic archaea in Sulfolobales publication-title: Biosci Biotechnol Biochem – volume: 6 start-page: 493 year: 2013 end-page: 502 article-title: Trends in bacterial trehalose metabolism and significant nodes of metabolic pathway in the direction of trehalose accumulation publication-title: Microb Biotechnol – volume: 185 start-page: 4233 year: 2003 end-page: 4242 article-title: Mechanisms of activation of phosphoenolpyruvate carboxykinase from by Ca and of desensitization by trypsin publication-title: J Bacteriol – volume: 180 start-page: 3421 year: 1998 end-page: 3431 article-title: Cloning, sequencing, and phenotypic characterization of the gene from KT2440 publication-title: J Bacteriol – volume: 43 start-page: D439 year: 2015 end-page: D446 article-title: BRENDA in 2015: exciting developments in its 25th year of existence publication-title: Nucleic Acids Res – volume: 146 start-page: 199 year: 2000 end-page: 208 article-title: Three pathways for trehalose biosynthesis in mycobacteria publication-title: Microbiology – volume: 2 start-page: 144 year: 2006 end-page: 148 article-title: Completing the uric acid degradation pathway through phylogenetic comparison of whole genomes publication-title: Nat Chem Biol – volume: 5 start-page: 231 year: 2014 article-title: How drugs get into cells: tested and testable predictions to help discriminate between transporter‐mediated uptake and lipoidal bilayer diffusion publication-title: Front Pharmacol – volume: 43 start-page: D459 year: 2015 end-page: D464 article-title: Updates in Rhea–a manually curated resource of biochemical reactions publication-title: Nucleic Acids Res – volume: 46 start-page: 59 year: 2000 end-page: 71 article-title: Characterization and overproduction of the encoded bifunctional enzyme that exhibits both phytase and acid phosphatase activities publication-title: Can J Microbiol – volume: 190 start-page: 2690 year: 2008 end-page: 2699 article-title: Identification of two gene clusters and a transcriptional regulator required for glycine betaine catabolism publication-title: J Bacteriol – volume: 339 start-page: 157 year: 1989 end-page: 158 article-title: Sleuthing out bacterial identities publication-title: Nature – volume: 11 start-page: 1246 year: 2001 end-page: 1255 article-title: Phenotype microarrays for high‐throughput phenotypic testing and assay of gene function publication-title: Genome Res – volume: 184 start-page: 4246 year: 2002 end-page: 4258 article-title: pH‐dependent expression of periplasmic proteins and amino acid catabolism in publication-title: J Bacteriol – volume: 78 start-page: 13 year: 2010 end-page: 34 article-title: The BCCT family of carriers: from physiology to crystal structure publication-title: Mol Microbiol – volume: 184 start-page: 2837 year: 2002 end-page: 2840 article-title: The gene of publication-title: J Bacteriol – volume: 9 start-page: e110038 year: 2014 article-title: Draft genome sequence analysis of a W15Oct28 strain with antagonistic activity to Gram‐positive and sp. pathogens publication-title: PLoS One – volume: 278 start-page: 26458 year: 2003 end-page: 26465 article-title: Why is trehalose an exceptional protein stabilizer? An analysis of the thermal stability of proteins in the presence of the compatible osmolyte trehalose publication-title: J Biol Chem – volume: 43 start-page: D261 year: 2015 end-page: D269 article-title: Expanded microbial genome coverage and improved protein family annotation in the COG database publication-title: Nucleic Acids Res – volume: 9 start-page: e98367 year: 2014 article-title: The gluconeogenesis pathway is involved in maintenance of enterohaemorrhagic O157:H7 in bovine intestinal content publication-title: PLoS One – ident: e_1_2_6_129_1 doi: 10.1111/j.1574-6976.2010.00249.x – ident: e_1_2_6_25_1 doi: 10.1111/j.1365-2958.2009.06962.x – ident: e_1_2_6_28_1 doi: 10.1111/1462-2920.12270 – ident: e_1_2_6_83_1 doi: 10.1074/jbc.M502585200 – ident: e_1_2_6_75_1 doi: 10.1111/j.1462-2920.2010.02331.x – ident: e_1_2_6_24_1 doi: 10.1128/JB.01585-07 – ident: e_1_2_6_42_1 doi: 10.1139/cjm-46-1-59 – ident: e_1_2_6_121_1 doi: 10.1186/1472-6750-13-93 – ident: e_1_2_6_20_1 doi: 10.1093/emboj/16.19.5922 – ident: e_1_2_6_8_1 doi: 10.1093/nar/gks1193 – ident: e_1_2_6_98_1 doi: 10.1074/jbc.M801195200 – ident: e_1_2_6_110_1 doi: 10.1128/jb.170.7.3142-3149.1988 – ident: e_1_2_6_78_1 doi: 10.1093/nar/gku961 – ident: e_1_2_6_49_1 doi: 10.1046/j.1462-2920.2002.00370.x – ident: e_1_2_6_130_1 doi: 10.1073/pnas.1501384112 – ident: e_1_2_6_29_1 doi: 10.1111/1758-2229.12223 – ident: e_1_2_6_7_1 doi: 10.1007/s12038-007-0055-7 – ident: e_1_2_6_13_1 doi: 10.1371/journal.pone.0098367 – volume: 65 start-page: 4837 year: 1999 ident: e_1_2_6_88_1 article-title: Biochemical and genetic analyses of ferulic acid catabolism in Pseudomonas sp. strain HR199 publication-title: Appl Environ Microbiol doi: 10.1128/AEM.65.11.4837-4847.1999 – ident: e_1_2_6_6_1 doi: 10.1111/j.1462-2920.2007.01464.x – ident: e_1_2_6_39_1 doi: 10.1093/nar/gku1223 – ident: e_1_2_6_14_1 doi: 10.1016/B978-0-12-800143-1.00002-6 – ident: e_1_2_6_103_1 doi: 10.1111/1751-7915.12029 – ident: e_1_2_6_43_1 doi: 10.1038/sj.emboj.7601041 – ident: e_1_2_6_120_1 doi: 10.1093/nar/gks1194 – ident: e_1_2_6_92_1 doi: 10.1093/nar/gku1002 – ident: e_1_2_6_4_1 doi: 10.1073/pnas.062526999 – ident: e_1_2_6_59_1 doi: 10.1271/bbb.60.1720 – ident: e_1_2_6_86_1 doi: 10.1371/journal.pcbi.1001116 – ident: e_1_2_6_126_1 doi: 10.1128/JB.01393-07 – ident: e_1_2_6_124_1 doi: 10.1128/AEM.03565-12 – ident: e_1_2_6_9_1 doi: 10.1038/nature08480 – ident: e_1_2_6_47_1 doi: 10.15252/msb.20145697 – ident: e_1_2_6_65_1 doi: 10.1007/s00253-004-1862-5 – ident: e_1_2_6_95_1 doi: 10.1371/journal.pcbi.1000210 – ident: e_1_2_6_122_1 doi: 10.1007/s00203-005-0054-8 – ident: e_1_2_6_41_1 doi: 10.1074/jbc.274.53.37901 – ident: e_1_2_6_55_1 doi: 10.3389/fphar.2014.00231 – ident: e_1_2_6_104_1 doi: 10.1529/biophysj.106.084343 – ident: e_1_2_6_112_1 doi: 10.1002/biot.201000124 – ident: e_1_2_6_97_1 doi: 10.1038/nchembio768 – ident: e_1_2_6_105_1 doi: 10.1038/nprot.2011.308 – ident: e_1_2_6_101_1 doi: 10.1128/jb.178.10.2804-2812.1996 – ident: e_1_2_6_35_1 doi: 10.1186/1471-2164-13-69 – volume: 267 start-page: 10433 year: 1992 ident: e_1_2_6_96_1 article-title: NhaR, a protein homologous to a family of bacterial regulatory proteins (LysR), regulates nhaA, the sodium proton antiporter gene in Escherichia coli publication-title: J Biol Chem doi: 10.1016/S0021-9258(19)50037-0 – ident: e_1_2_6_54_1 doi: 10.1074/jbc.M300815200 – ident: e_1_2_6_60_1 doi: 10.1006/jmbi.2000.4315 – ident: e_1_2_6_62_1 doi: 10.1111/1462-2920.12812 – ident: e_1_2_6_115_1 doi: 10.1093/nar/gku989 – ident: e_1_2_6_119_1 doi: 10.1111/1462-2920.13015 – ident: e_1_2_6_63_1 doi: 10.1093/nar/gkm160 – ident: e_1_2_6_69_1 doi: 10.1093/nar/25.5.955 – ident: e_1_2_6_73_1 doi: 10.1093/nar/gkp698 – start-page: 141 volume-title: Bergey's Manual of Systematic Bacteriology year: 1984 ident: e_1_2_6_90_1 – ident: e_1_2_6_118_1 doi: 10.1371/journal.pgen.1000344 – ident: e_1_2_6_107_1 doi: 10.1128/jb.178.11.3362-3364.1996 – ident: e_1_2_6_32_1 doi: 10.1111/j.1462-2920.2004.00734.x – ident: e_1_2_6_81_1 doi: 10.1074/jbc.M115.687749 – ident: e_1_2_6_44_1 doi: 10.1093/nar/gks1146 – ident: e_1_2_6_57_1 doi: 10.1002/pmic.200500329 – ident: e_1_2_6_68_1 doi: 10.1093/bioinformatics/btp352 – ident: e_1_2_6_99_1 doi: 10.1128/JB.180.13.3421-3431.1998 – ident: e_1_2_6_37_1 doi: 10.1038/nrmicro1021 – ident: e_1_2_6_72_1 doi: 10.1128/JB.184.10.2837-2840.2002 – ident: e_1_2_6_67_1 doi: 10.1073/pnas.0405375101 – ident: e_1_2_6_132_1 doi: 10.1093/nar/gkq1093 – ident: e_1_2_6_40_1 doi: 10.1093/bioinformatics/btt036 – ident: e_1_2_6_93_1 doi: 10.1038/nmeth.1701 – ident: e_1_2_6_5_1 doi: 10.1186/gb-2010-11-10-r106 – ident: e_1_2_6_64_1 doi: 10.1371/journal.pcbi.1003118 – ident: e_1_2_6_114_1 doi: 10.1128/JB.185.14.4233-4242.2003 – ident: e_1_2_6_71_1 doi: 10.1016/S0005-2736(99)00085-1 – ident: e_1_2_6_2_1 doi: 10.1016/j.tig.2012.11.001 – ident: e_1_2_6_56_1 doi: 10.1093/nar/gks1027 – ident: e_1_2_6_89_1 doi: 10.1016/j.bbamem.2005.09.010 – ident: e_1_2_6_102_1 doi: 10.1128/jb.178.6.1663-1670.1996 – ident: e_1_2_6_116_1 doi: 10.1093/nar/gkt900 – ident: e_1_2_6_30_1 doi: 10.1099/00221287-146-1-199 – ident: e_1_2_6_127_1 doi: 10.1023/A:1012275512136 – ident: e_1_2_6_58_1 doi: 10.1111/1758-2229.12090 – ident: e_1_2_6_61_1 doi: 10.1371/journal.pcbi.1000308 – ident: e_1_2_6_100_1 doi: 10.1046/j.1462-2920.2002.00368.x – ident: e_1_2_6_19_1 doi: 10.1093/nar/gks1005 – ident: e_1_2_6_79_1 doi: 10.1046/j.1462-2920.2002.00366.x – ident: e_1_2_6_48_1 doi: 10.1186/1471-2105-11-119 – ident: e_1_2_6_45_1 doi: 10.1093/database/bat059 – ident: e_1_2_6_21_1 doi: 10.1093/nar/gkt1103 – ident: e_1_2_6_10_1 doi: 10.1038/nchembio.1387 – ident: e_1_2_6_109_1 doi: 10.1016/0022-2836(81)90087-5 – ident: e_1_2_6_46_1 doi: 10.1128/JB.01178-10 – ident: e_1_2_6_87_1 doi: 10.1073/pnas.0601119103 – ident: e_1_2_6_77_1 doi: 10.1111/j.1462-2920.2010.02166.x – ident: e_1_2_6_117_1 doi: 10.1128/jb.172.8.4339-4347.1990 – ident: e_1_2_6_106_1 doi: 10.1016/j.bbapap.2008.01.005 – ident: e_1_2_6_66_1 doi: 10.1007/978-1-61779-412-4_15 – ident: e_1_2_6_82_1 doi: 10.1101/gr.194201 – ident: e_1_2_6_33_1 doi: 10.1128/JB.183.2.644-653.2001 – ident: e_1_2_6_123_1 doi: 10.1046/j.1365-2958.2003.03547.x – ident: e_1_2_6_125_1 doi: 10.1099/mic.0.028787-0 – ident: e_1_2_6_94_1 doi: 10.1016/S0021-9258(18)53913-2 – ident: e_1_2_6_15_1 doi: 10.1038/339157a0 – ident: e_1_2_6_26_1 doi: 10.1016/S0167-4781(97)00097-3 – ident: e_1_2_6_38_1 doi: 10.1111/j.1462-2920.2011.02430.x – ident: e_1_2_6_53_1 doi: 10.4056/sigs.1794338 – ident: e_1_2_6_3_1 doi: 10.1093/oxfordjournals.molbev.a026410 – ident: e_1_2_6_80_1 doi: 10.1038/nrmicro3253 – ident: e_1_2_6_108_1 doi: 10.1111/j.1574-6976.2011.00269.x – ident: e_1_2_6_128_1 doi: 10.1093/nar/gkq869 – ident: e_1_2_6_27_1 doi: 10.1093/nar/gkg847 – ident: e_1_2_6_31_1 doi: 10.1093/genetics/54.1.61 – ident: e_1_2_6_111_1 doi: 10.1371/journal.pcbi.1002540 – ident: e_1_2_6_16_1 doi: 10.1101/gr.186501 – ident: e_1_2_6_36_1 doi: 10.1016/S1369-5274(99)80030-7 – ident: e_1_2_6_133_1 doi: 10.1111/j.1365-2958.2010.07332.x – ident: e_1_2_6_70_1 doi: 10.1111/1574-6976.12076 – ident: e_1_2_6_18_1 doi: 10.1152/ajpcell.00360.2004 – ident: e_1_2_6_22_1 doi: 10.1099/mic.0.044263-0 – ident: e_1_2_6_52_1 doi: 10.1128/JB.00968-07 – ident: e_1_2_6_85_1 doi: 10.1111/j.1365-2958.2010.07448.x – ident: e_1_2_6_131_1 doi: 10.1371/journal.pone.0110038 – ident: e_1_2_6_23_1 doi: 10.1093/nar/gku1068 – ident: e_1_2_6_113_1 doi: 10.1128/JB.184.15.4246-4258.2002 – ident: e_1_2_6_51_1 doi: 10.1128/jb.174.3.889-898.1992 – ident: e_1_2_6_74_1 doi: 10.1016/j.pep.2003.07.006 – ident: e_1_2_6_50_1 doi: 10.1073/pnas.0802273105 – ident: e_1_2_6_84_1 doi: 10.1186/1752-0509-2-79 – ident: e_1_2_6_91_1 doi: 10.1016/S0167-4838(00)00214-4 – ident: e_1_2_6_11_1 doi: 10.1128/JB.00666-12 – ident: e_1_2_6_12_1 doi: 10.1093/bib/bbs058 – ident: e_1_2_6_76_1 doi: 10.1093/nar/gku1243 – ident: e_1_2_6_17_1 doi: 10.1093/nar/gkg590 – ident: e_1_2_6_34_1 doi: 10.1074/jbc.M109.033944 |
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By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al., ) this bacterium was... By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al ., ) this bacterium was considered... By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al., ) this bacterium was considered... Summary By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al., ) this bacterium was... By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al.,) this bacterium was considered a... By the time the complete genome sequence of the soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al., 2002) this bacterium was... |
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| SubjectTerms | Bacterial Proteins - genetics Bacterial Proteins - metabolism biochemical pathways Biochemistry, Molecular Biology Bioremediation Biotechnology carbon Carbon - metabolism genes Genetics Genome, Bacterial Genomes Genomics Industrial wastes Life Sciences Metabolism nitrogen Nitrogen - metabolism nucleotide sequences phosphorus Pseudomonas putida Pseudomonas putida - genetics Pseudomonas putida - metabolism Redox reactions Rhizosphere soil bacteria stress tolerance Systeem en Synthetische Biologie Systems and Synthetic Biology VLAG |
| Title | The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis |
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