1887

Journal of Medical Microbiology logo

Volume 69, Issue 3

Narrative of a versatile and adept species Free

Abstract

is a fast-growing bacterium found mostly in temperate soil and water habitats. The metabolic versatility of makes this organism attractive for biotechnological applications such as biodegradation of environmental pollutants and synthesis of added-value chemicals (biocatalysis). This organism has been extensively studied in respect to various stress responses, mechanisms of genetic plasticity and transcriptional regulation of catabolic genes. is able to colonize the surface of living organisms, but is generally considered to be of low virulence. A number of strains are able to promote plant growth. The aim of this review is to give historical overview of the discovery of the species and isolation and characterization of strains displaying potential for biotechnological applications. This review also discusses some major findings in research encompassing regulation of catabolic operons, stress-tolerance mechanisms and mechanisms affecting evolvability of bacteria under conditions of environmental stress.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): biodegradation , biotechnology , evolution , interactions with eukaryotic hosts , species Pseudomonas putida and stress tolerance
Funding
This study was supported by the:
  • Eesti Teadusagentuur (Award IUT20-19)
    • Principle Award Recipient: Maia Kivisaar
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.001137
2020-01-20
2024-05-13
Loading full text...

Full text loading...

/deliver/fulltext/jmm/69/3/324.html?itemId=/content/journal/jmm/10.1099/jmm.0.001137&mimeType=html&fmt=ahah

References

  1. Silby MW, Winstanley C, Godfrey SAC, Levy SB, Jackson RW. Pseudomonas genomes: diverse and adaptable. FEMS Microbiol Rev 2011; 35:652–680 [View Article]
     [Google Scholar]
  2. Udaondo Z, Duque E, Fernández M, Molina L, de la Torre J et al. Analysis of solvent tolerance in Pseudomonas putida DOT-T1E based on its genome sequence and a collection of mutants. FEBS Lett 2012; 586:2932–2938 [View Article]
     [Google Scholar]
  3. Ramos JL, Gallegos MT, Marqués S, Ramos-González MI, Espinosa-Urgel M et al. Responses of gram-negative bacteria to certain environmental stressors. Curr Opin Microbiol 2001; 4:166–171 [View Article]
     [Google Scholar]
  4. Timmis KN, Steffan RJ, Unterman R. Designing microorganisms for the treatment of toxic wastes. Annu Rev Microbiol 1994; 48:525–557 [View Article]
     [Google Scholar]
  5. dos Santos VAPM, Heim S, Moore ERB, Stratz M, Timmis KN. Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ Microbiol 2004; 6:1264–1286 [View Article]
     [Google Scholar]
  6. Nikel PI, de Lorenzo V. Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism. Metab Eng 2018; 50:142155 [View Article]
     [Google Scholar]
  7. Matilla MA, Pizarro-Tobias P, Roca A, Fernandez M, Duque E et al. Complete Genome of the Plant Growth-Promoting Rhizobacterium Pseudomonas putida BIRD-1. J Bacteriol 2011; 193:1290 [View Article]
     [Google Scholar]
  8. Roca A, Pizarro-Tobías P, Udaondo Z, Fernández M, Matilla MA et al. Analysis of the plant growth-promoting properties encoded by the genome of the rhizobacterium Pseudomonas putida BIRD-1. Environ Microbiol 2013; 15:780–794 [View Article]
     [Google Scholar]
  9. Parte AC. LPSN – list of prokaryotic names with standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article]
     [Google Scholar]
  10. Palleroni NJ. Genus I. Pseudomonas Migula 1984. In Brenner DJ, Krieg NR, Staley JT. (editors) Bergey's Manual of Systematic Bacteriology, 2nd ed. New York, USA: Springer; 2005 pp 323–379
     [Google Scholar]
  11. Migula W. Über ein neues system Der Bakterien. Arb Bakteriol Inst Karlsruhe 1984; 1:235–328
     [Google Scholar]
  12. Palleroni NJ, Moore ERB. Taxonomy of Pseudomonads: Experimental Approaches. In Ramos JL. editor Pseudomonas Genomics, Life Style and Molecular Architecture NeW York, USA: Kluwer Academic/Plenum Publishers; 2004 pp 3–44
     [Google Scholar]
  13. Palleroni NJ. The Pseudomonas story. Environ Microbiol 2010; 12:1377–1383 [View Article]
     [Google Scholar]
  14. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM. Bergey's manual of Determinative Bacteriology, 1st ed. Baltimore, USA: Williams and Wilkins; 1923
     [Google Scholar]
  15. Peix A, Ramírez-Bahena M-H, Velázquez E. The current status on the taxonomy of Pseudomonas revisited: An update. Infection, Genetics and Evolution 2018; 57:106–116 [View Article]
     [Google Scholar]
  16. Stanier RY, Palleroni NJ, Doudoroff M. The aerobic pseudomonads a taxonomic study. J Gen Microbiol 1966; 43:159–271 [View Article]
     [Google Scholar]
  17. Palleroni NJ, Kunisawa R, Contopoulou R, Doudoroff M. Nucleic acid homologies in the genus Pseudomonas . Int J Syst Bacteriol 1973; 23:333–339 [View Article]
     [Google Scholar]
  18. Kersters K, Ludwig W, Vancanneyt M, De Vos P, Gillis M et al. Recent changes in the classification of the pseudomonads: an overview. Syst Appl Microbiol 1996; 19:465–477 [View Article]
     [Google Scholar]
  19. Palleroni NJ. Prokaryote taxonomy of the 20th century and the impact of studies on the genus Pseudomonas: a personal view. Microbiology 2003; 149:1–7 [View Article]
     [Google Scholar]
  20. Bennasar A, Mulet M, Lalucat J, García-Valdés E. PseudoMLSA: a database for multigenic sequence analysis of Pseudomonas species. BMC Microbiol 2010; 10:118 [View Article]
     [Google Scholar]
  21. Mulet M, Lalucat J, Garcia-Valdes E. DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 2010; 12:1513–1530
     [Google Scholar]
  22. Mulet M, García-Valdés E, Lalucat J. Phylogenetic affiliation of Pseudomonas putida biovar A and B strains. Res Microbiol 2013; 164:351–359 [View Article]
     [Google Scholar]
  23. Gomila M, Mulet M, Lalucat J, García-Valdés E. Phylogenomics and systematics in Pseudomonas . Front Microbiol 2015; 6:214 [View Article]
     [Google Scholar]
  24. Hesse C, Schulz F, Bull CT, Shaffer BT, Yan Q et al. Genome‐based evolutionary history of Pseudomonas spp. Environ Microbiol 2018; 20:2142–2159 [View Article]
     [Google Scholar]
  25. Keshavarz-Tohid V, Vacheron J, Dubost A, Prigent-Combaret C, Taheri P et al. Genomic, phylogenetic and catabolic re-assessment of the Pseudomonas putida clade supports the delineation of Pseudomonas alloputida sp. nov., Pseudomonas inefficax sp. nov., Pseudomonas persica sp. nov., and Pseudomonas shirazica sp. nov. Syst Appl Microbiol 2019; 42:468–480 [View Article]
     [Google Scholar]
  26. Tran PN, Savka MA, Gan HM. In-silico taxonomic classification of 373 genomes reveals species misidentification and new genospecies within the Genus Pseudomonas . Front Microbiol 2017; 8:1296 [View Article]
     [Google Scholar]
  27. Yonezuka K, Shimodaira J, Tabata M, Ohji S, Hosoyama A et al. Phylogenetic analysis reveals the taxonomically diverse distribution of the Pseudomonas putida group. J Gen Appl Microbiol 2017; 63:1–10 [View Article]
     [Google Scholar]
  28. Liffourrena AS, Lucchesi GI, Identification LGI. Identification, cloning and biochemical characterization of Pseudomonas putida A (ATCC 12633) monooxygenase enzyme necessary for the metabolism of tetradecyltrimethylammonium bromide. Appl Biochem Biotechnol 2014; 173:552–561 [View Article]
     [Google Scholar]
  29. Liffourrena AS, Salvano MA, Lucchesi GI. Pseudomonas putida a ATCC 12633 oxidizes trimethylamine aerobically via two different pathways. Arch Microbiol 2010; 192:471–476 [View Article]
     [Google Scholar]
  30. Regenhardt D, Heuer H, Heim S, Fernandez DU, Strompl C et al. Pedigree and taxonomic credentials of Pseudomonas putida strain KT2440. Environ Microbiol 2002; 4:912–915 [View Article]
     [Google Scholar]
  31. Nikel PI, de Lorenzo V. Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism. Metab Eng 2018; 50:142–155 [View Article]
     [Google Scholar]
  32. Martínez-García E, Nikel PI, Aparicio T, de Lorenzo V. Pseudomonas 2.0: genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression. Microb Cell Fact 2014; 13:159 [View Article]
     [Google Scholar]
  33. Nikel PI, Martínez-García E, de Lorenzo V. Biotechnological domestication of pseudomonads using synthetic biology. Nat Rev Microbiol 2014; 12:368–379 [View Article]
     [Google Scholar]
  34. Ramos JL, Marqués S, Timmis KN. Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annu Rev Microbiol 1997; 51:341–373 [View Article]
     [Google Scholar]
  35. Espinosa-Urgel M, Kolter R, Ramos J-L. Root colonization by Pseudomonas putida: love at first sight. Microbiology 2002; 148:341–343 [View Article]
     [Google Scholar]
  36. Nogales J, Palsson Bernhard Ø, Thiele I, Palsson BO. A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol 2008; 2:79 [View Article]
     [Google Scholar]
  37. Puchałka J, Oberhardt MA, Godinho M, Bielecka A, Regenhardt D et al. Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Comput Biol 2008; 4:e1000210 [View Article]
     [Google Scholar]
  38. Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H et al. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 2002; 4:799–808 [View Article]
     [Google Scholar]
  39. Bagdasarian M, Lurz R, Rückert B, Franklin FCH, Bagdasarian MM et al. Specific-purpose plasmid cloning vectors II. broad host range, high copy number, RSF 1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas . Gene 1981; 16:237–247 [View Article]
     [Google Scholar]
  40. Nakazawa T. Travels of a Pseudomonas, from Japan around the world. Environ Microbiol 2002; 4:782–786 [View Article]
     [Google Scholar]
  41. Bayley SA, Duggleby CJ, Worsey MJ, Williams PA, Hardy KG et al. Two modes of loss of the TOL function from Pseudomonas putida MT-2. Molec. Gen. Genet. 1977; 154:203–204 [View Article]
     [Google Scholar]
  42. Shima H, Kudo T, Horikoshi K. Isolation of toluene-resistant mutants from Pseudomonas putida PpG1(ATCC 17453). Agric Biol Chem 1991; 55:1197–1199 [View Article]
     [Google Scholar]
  43. Cruden DL, Wolfram JH, Rogers RD, Gibson DT. Physiological properties of a Pseudomonas strain which grows with p-xylene in a two-phase (organic-aqueous) medium. Appl Environ Microbiol 1992; 58:2723–2729
     [Google Scholar]
  44. Weber FJ, Ooijkaas LP, Schemen RM, Hartmans S, de Bont JA. Adaptation of Pseudomonas putida S12 to high concentrations of styrene and other organic solvents. Appl Environ Microbiol 1993; 59:3502–3504
     [Google Scholar]
  45. Ramos JL, Duque E, Huertas MJ, Haïdour A. Isolation and expansion of the catabolic potential of a Pseudomonas putida strain able to grow in the presence of high concentrations of aromatic hydrocarbons. J Bacteriol 1995; 177:3911–3916 [View Article]
     [Google Scholar]
  46. Taghavi S, Barac T, Greenberg B, Borremans B, Vangronsveld J et al. Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene. Appl Environ Microbiol 2005; 71:8500–8505 [View Article]
     [Google Scholar]
  47. Choi EN, Cho MC, Kim Y, Kim CK, Lee K. Expansion of growth substrate range in Pseudomonas putida F1 by mutations in both cymR and todS, which recruit a ring-fission hydrolase CmtE and induce the tod catabolic operon, respectively. Microbiology 2003; 149:795–805 [View Article]
     [Google Scholar]
  48. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
     [Google Scholar]
  49. Diaz E. Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility. International Microbiology: the Official Journal of the Spanish Society for Microbiology 2004; 7:173–180
     [Google Scholar]
  50. Harwood CS, Parales RE. The β-KETOADIPATE pathway and the biology of self-identity. Annu Rev Microbiol 1996; 50:553–590 [View Article]
     [Google Scholar]
  51. Ornston LN. Regulation of catabolic pathways in Pseudomonas . Bacteriological reviews 1971; 35:87–116
     [Google Scholar]
  52. Williams PA, Jones RM, Zylstra G. Genomics of catabolic plasmids. In Ramos JL. editor Pseudomonas Genomics, Lifestyle and Molecular Architecture New York, USA: Kluwer Academic/Plenum Publishers; 2004 pp 165–195
     [Google Scholar]
  53. Rheinwald JG, Chakrabarty AM, Gunsalus IC. A transmissible plasmid controlling camphor oxidation in Pseudomonas putida . Proc Natl Acad Sci U S A 1973; 70:885–889 [View Article]
     [Google Scholar]
  54. Chakrabarty AM. Genetic basis of the biodegradation of salicylate in Pseudomonas . J Bacteriol 1972; 112:815–823
     [Google Scholar]
  55. Dunn NW, Gunsalus IC. Transmissible plasmid coding early enzymes of naphthalene oxidation in Pseudomonas putida . J Bacteriol 1973; 114:974–979
     [Google Scholar]
  56. Williams PA, Murray K. Metabolism of benzoate and the methylbenzoates by Pseudomonas putida (arvilla) mt-2: evidence for the existence of a TOL plasmid. J Bacteriol 1974; 120:416–423
     [Google Scholar]
  57. Wong CL, Dunn NW. Transmissible plasmid coding for the degradation of benzoate and m -toluate in Pseudomonas arvilla mt-2. Genet Res 1974; 23:227–232 [View Article]
     [Google Scholar]
  58. Cases I, de Lorenzo V. Promoters in the environment: transcriptional regulation in its natural context. Nat Rev Microbiol 2005; 3:105–118 [View Article]
     [Google Scholar]
  59. Herrmann H, Janke D, Krejsa S, Roy M. In vivo generation of R68.45-pPGH1 hybrid plasmids conferring a Phl+ (meta pathway) phenotype. Mol Gen Genet 1988; 214:173–176 [View Article]
     [Google Scholar]
  60. Shingler V, Franklin FC, Tsuda M, Holroyd D, Bagdasarian M. Molecular analysis of a plasmid-encoded phenol hydroxylase from Pseudomonas CF600. J Gen Microbiol 1989; 135:1083–1092
     [Google Scholar]
  61. Kivisaar MA, Habicht JK, Heinaru AL. Degradation of phenol and m-toluate in Pseudomonas sp. strain EST1001 and its Pseudomonas putida transconjugants is determined by a multiplasmid system. J Bacteriol 1989; 171:5111–5116 [View Article]
     [Google Scholar]
  62. Chakrabarty AM. Bioengineered bugs, drugs and contentious issues in patenting. Bioeng Bugs 2010; 1:2–8 [View Article]
     [Google Scholar]
  63. Chakrabarty AM inventor. Microorganisms having multiple compatible degradative energy-generating plasmids and preparation thereof United States; 1981
  64. Cases I, Lorenzo de V. Genetically modified organisms for the environment: stories of success and failure and what we have learned from them. International Microbiology: the Official Journal of the Spanish Society for Microbiology 2005; 8:213–222
     [Google Scholar]
  65. Pieper DH, Reineke W. Engineering bacteria for bioremediation. Curr Opin Biotechnol 2000; 11:262–270 [View Article]
     [Google Scholar]
  66. Shingler V. Integrated regulation in response to aromatic compounds: from signal sensing to attractive behaviour. Environ Microbiol 2003; 5:1226–1241 [View Article]
     [Google Scholar]
  67. Cases I, Lorenzo de V. New EMBO members' review: the black cat/white cat principle of signal integration in bacterial promoters. EMBO J 2001; 20:1–11 [View Article]
     [Google Scholar]
  68. Bertoni G, Fujita N, Ishihama A, Lorenzo de V. Active recruitment of sigma 54-RNA polymerase to the Pu promoter of Pseudomonas putida: role of IHF and alpha CTD. EMBO J 1998; 17:5120–5128 [View Article]
     [Google Scholar]
  69. Shingler V, Bartilson M, Moore T. Cloning and nucleotide sequence of the gene encoding the positive regulator (DmpR) of the phenol catabolic pathway encoded by pVI150 and identification of DmpR as a member of the NtrC family of transcriptional activators. J Bacteriol 1993; 175:1596–1604 [View Article]
     [Google Scholar]
  70. Fernández S, Shingler V, De Lorenzo V. Cross-regulation by XylR and DmpR activators of Pseudomonas putida suggests that transcriptional control of biodegradative operons evolves independently of catabolic genes. J Bacteriol 1994; 176:5052–5058 [View Article]
     [Google Scholar]
  71. Sze CC, Bernardo LMD, Shingler V. Integration of Global Regulation of Two Aromatic-Responsive 54-Dependent Systems: a Common Phenotype by Different Mechanisms. J Bacteriol 2002; 184:760–770 [View Article]
     [Google Scholar]
  72. Rothmel RK, Aldrich TL, Houghton JE, Coco WM, Ornston LN et al. Nucleotide sequencing and characterization of Pseudomonas putida catR: a positive regulator of the catBC operon is a member of the LysR family. J Bacteriol 1990; 172:922–931 [View Article]
     [Google Scholar]
  73. Coco WM, Rothmel RK, Henikoff S, Chakrabarty AM. Nucleotide sequence and initial functional characterization of the clcR gene encoding a LysR family activator of the clcABD chlorocatechol operon in Pseudomonas putida . J Bacteriol 1993; 175:417–427 [View Article]
     [Google Scholar]
  74. Parsek MR, McFall SM, Shinabarger DL, Chakrabarty AM. Interaction of two LysR-type regulatory proteins CatR and ClcR with heterologous promoters: functional and evolutionary implications. Proc Natl Acad Sci U S A 1994; 91:12393–12397 [View Article]
     [Google Scholar]
  75. McFall SM, Chugani SA, Chakrabarty AM. Transcriptional activation of the catechol and chlorocatechol operons: variations on a theme. Gene 1998; 223:257–267
     [Google Scholar]
  76. Kasak L, Hôrak R, Nurk A, Talvik K, Kivisaar M. Regulation of the catechol 1,2-dioxygenase- and phenol monooxygenase-encoding pheBA operon in Pseudomonas putida PaW85. J Bacteriol 1993; 175:8038–8042 [View Article]
     [Google Scholar]
  77. Tover A, Kivisaar M, Chakrabarty AM, Chugani SA, Zernant J. Critical nucleotides in the interaction of CatR with the pheBA promoter: conservation of the CatR-mediated regulation mechanisms between the pheBA and catBCA operons. Microbiology 2000; 146:173–183 [View Article]
     [Google Scholar]
  78. Parsek MR, Kivisaar M, Chakrabarty AM. Differential DNA bending introduced by the Pseudomonas putida LysR-type regulator, CatR, at the plasmid-borne pheBA and chromosomal catBC promoters. Mol Microbiol 1995; 15:819–829 [View Article]
     [Google Scholar]
  79. Peters M, Heinaru E, Talpsep E, Wand H, Stottmeister U et al. Acquisition of a deliberately introduced phenol degradation operon, pheBA, by different indigenous Pseudomonas species. App Environ Microbiol 1997; 63:4899–4906
     [Google Scholar]
  80. Heinaru E, Truu J, Stottmeister U, Heinaru A. Three types of phenol and p-cresol catabolism in phenol- and p-cresol-degrading bacteria isolated from river water continuously polluted with phenolic compounds. FEMS Microbiol Ecol 2000; 31:195–205 [View Article]
     [Google Scholar]
  81. Peters M, Tomikas A, Nurk A. Organization of the horizontally transferred pheBA operon and its adjacent genes in the genomes of eight indigenous Pseudomonas strains. Plasmid 2004; 52:230–236 [View Article]
     [Google Scholar]
  82. Hazen TC, Stahl DA. Using the stress response to monitor process control: pathways to more effective bioremediation. Curr Opin Biotechnol 2006; 17:285–290 [View Article]
     [Google Scholar]
  83. Roszak DB, Colwell RR. Survival strategies of bacteria in the natural environment. Microbiol Rev 1987; 51:365–379
     [Google Scholar]
  84. Ramos J-L, Sol Cuenca M, Molina-Santiago C, Segura A, Duque E et al. Mechanisms of solvent resistance mediated by interplay of cellular factors in Pseudomonas putida . FEMS Microbiol Rev 2015; 39:555–566 [View Article]
     [Google Scholar]
  85. Inoue A, Horikoshi K. A Pseudomonas thrives in high concentrations of toluene. Nature 1989; 338:264–266 [View Article]
     [Google Scholar]
  86. Ramos JL, Duque E, Gallegos M-T, Godoy P, Ramos-González MI et al. Mechanisms of solvent tolerance in gram-negative bacteria. Annu Rev Microbiol 2002; 56:743–768 [View Article]
     [Google Scholar]
  87. Heipieper HJ, Meinhardt F, Segura A. The cis-trans isomerase of unsaturated fatty acids in Pseudomonas and Vibrio: biochemistry, molecular biology and physiological function of a unique stress adaptive mechanism. FEMS Microbiol Lett 2003; 229:1–7 [View Article]
     [Google Scholar]
  88. Fernandes P, Ferreira BS, Cabral JM. Solvent tolerance in bacteria: role of efflux pumps and cross-resistance with antibiotics. Int J Antimicrob Agents 2003; 22:211–216 [View Article]
     [Google Scholar]
  89. Domínguez-Cuevas P, González-Pastor J-E, Marqués S, Ramos J-L, de Lorenzo V. Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene. J Biol Chem 2006; 281:11981–11991 [View Article]
     [Google Scholar]
  90. Santos PM, Benndorf D, Sá-Correia I. Insights intoPseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics. Proteomics 2004; 4:2640–2652 [View Article]
     [Google Scholar]
  91. Kim J, Park W. Oxidative stress response in Pseudomonas putida . Appl Microbiol Biotechnol 2014; 98:6933–6946 [View Article]
     [Google Scholar]
  92. Kivistik PA, Putrinš M, Püvi K, Ilves H, Kivisaar M et al. The ColRS two-component system regulates membrane functions and protects Pseudomonas putida against phenol. J Bacteriol 2006; 188:8109–8117 [View Article]
     [Google Scholar]
  93. Putrinš M, Ilves H, Lilje L, Kivisaar M, Hõrak R. The impact of ColRS two-component system and TtgABC efflux pump on phenol tolerance of Pseudomonas putida becomes evident only in growing bacteria. BMC Microbiol 2010; 10:110 [View Article]
     [Google Scholar]
  94. Dekkers LC, Bloemendaal CJ, de Weger LA, Wijffelman CA, Spaink HP et al. A two-component system plays an important role in the root-colonizing ability of Pseudomonas fluorescens strain WCS365. Mol Plant Microbe Interact 1998; 11:45–56 [View Article]
     [Google Scholar]
  95. Ainsaar K, Mumm K, Ilves H, Hõrak R. The ColRS signal transduction system responds to the excess of external zinc, iron, manganese, and cadmium. BMC Microbiol 2014; 14:162 [View Article]
     [Google Scholar]
  96. Mumm K, Ainsaar K, Kasvandik S, Tenson T, Hõrak R. Responses of Pseudomonas putida to Zinc Excess Determined at the Proteome Level: Pathways Dependent and Independent of ColRS. J Proteome Res 2016; 15:4349–4368 [View Article]
     [Google Scholar]
  97. Putrinš M, Ilves H, Kivisaar M, Hõrak R. ColRS two-component system prevents lysis of subpopulation of glucose-grown Pseudomonas putida . Environ Microbiol 2008; 10:2886–2893 [View Article]
     [Google Scholar]
  98. Putrinš M, Ainelo A, Ilves H, Hõrak R. The ColRS system is essential for the hunger response of glucose-growing Pseudomonas putida . BMC Microbiol 2011; 11:170 [View Article]
     [Google Scholar]
  99. Ainsaar K, Tamman H, Kasvandik S, Tenson T, Hõrak R. The TonB m -PocAB System Is Required for Maintenance of Membrane Integrity and Polar Position of Flagella in Pseudomonas putida . J Bacteriol 2019; 201: [View Article]
     [Google Scholar]
  100. Trevors JT. Viable but non-culturable (VBNC) bacteria: gene expression in planktonic and biofilm cells. J Microbiol Methods 2011; 86:266–273 [View Article]
     [Google Scholar]
  101. Oliver JD. Recent findings on the viable but nonculturable state in pathogenic bacteria. FEMS Microbiol Rev 2010; 34:415–425 [View Article]
     [Google Scholar]
  102. Munoz-Rojas J, Bernal P, Duque E, Godoy P, Segura A et al. Involvement of cyclopropane fatty acids in the response of Pseudomonas putida KT2440 to freeze-drying. Appl Environ Microbiol 2006; 72:472–477 [View Article]
     [Google Scholar]
  103. Manzanera M, Garcia de Castro A, Tondervik A, Rayner-Brandes M, Strom AR et al. Hydroxyectoine is superior to trehalose for anhydrobiotic engineering of Pseudomonas putida KT2440. Appl Environ Microbiol 2002; 68:4328–4333 [View Article]
     [Google Scholar]
  104. Pazos-Rojas LA, Muñoz-Arenas LC, Rodríguez-Andrade O, López-Cruz LE, López-Ortega O et al. Desiccation-induced viable but nonculturable state in Pseudomonas putida KT2440, a survival strategy. PLoS One 2019; 14:e0219554 [View Article]
     [Google Scholar]
  105. Bailey J. Toward a science of metabolic engineering. Science 1991; 252:1668–1675 [View Article]
     [Google Scholar]
  106. Cases I, de Lorenzo V. Expression systems and physiological control of promoter activity in bacteria. Curr Opin Microbiol 1998; 1:303–310 [View Article]
     [Google Scholar]
  107. Ramos J, Wasserfallen A, Rose K, Timmis K. Redesigning metabolic routes: manipulation of TOL plasmid pathway for catabolism of alkylbenzoates. Science 1987; 235:593–596 [View Article]
     [Google Scholar]
  108. Wackett LP, Sadowsky MJ, Martinez B, Shapir N. Biodegradation of atrazine and related s-triazine compounds: from enzymes to field studies. Appl Microbiol Biotechnol 2002; 58:39–45 [View Article]
     [Google Scholar]
  109. Yuste L, Hervas AB, Canosa I, Tobes R, Jimenez JI et al. Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray. Environ Microbiol 2006; 8:165–177 [View Article]
     [Google Scholar]
  110. Reva ON, Weinel C, Weinel M, Bohm K, Stjepandic D et al. Functional genomics of stress response in Pseudomonas putida KT2440. J Bacteriol 2006; 188:4079–4092 [View Article]
     [Google Scholar]
  111. Kurbatov L, Albrecht D, Herrmann H, Petruschka L. Analysis of the proteome of Pseudomonas putida KT2440 grown on different sources of carbon and energy. Environ Microbiol 2006; 8:466–478 [View Article]
     [Google Scholar]
  112. Belda E, van Heck RGA, José Lopez-Sanchez M, Cruveiller S, Barbe V et al. The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis . Environ Microbiol 2016; 18:3403–3424 [View Article]
     [Google Scholar]
  113. Timmis KN. Pseudomonas putida: a cosmopolitan opportunist par excellence. Environ Microbiol 2002; 4:779–781 [View Article]
     [Google Scholar]
  114. Kampers LFC, Volkers RJM, Martins Dos Santos VAP. Pseudomonas putida KT2440 is HV1 certified, not GRAS. Microb Biotechnol 2019; 12:845–848
     [Google Scholar]
  115. Loeschcke A, Thies S. Pseudomonas putida—a versatile host for the production of natural products. Appl Microbiol Biotechnol 2015; 99:6197–6214 [View Article]
     [Google Scholar]
  116. Udaondo Z, Molina L, Daniels C, Gómez MJ, Molina-Henares MA et al. Metabolic potential of the organic-solvent tolerant Pseudomonas putida DOT-T1E deduced from its annotated genome. Microb Biotechnol 2013; 6:598–611 [View Article]
     [Google Scholar]
  117. Calero P, Nikel PI. Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms. Microb Biotechnol 2019; 12:98–124 [View Article]
     [Google Scholar]
  118. Spaans SK, Weusthuis RA, van der Oost J, Kengen Servé W. M., Kengen SW. NADPH-generating systems in bacteria and archaea. Front Microbiol 2015; 6:742 [View Article]
     [Google Scholar]
  119. Lemire J, Alhasawi A, Appanna VP, Tharmalingam S, Appanna VD. Metabolic defence against oxidative stress: the road less travelled so far. J Appl Microbiol 2017; 123:798–809 [View Article]
     [Google Scholar]
  120. Nikel PI, Chavarría M, Danchin A, de Lorenzo V. From dirt to industrial applications: Pseudomonas putida as a Synthetic Biology chassis for hosting harsh biochemical reactions. Curr Opin Chem Biol 2016; 34:20–29 [View Article]
     [Google Scholar]
  121. Martinez-Garcia E, Aparicio T, Lorenzo de V, Nikel PI. Engineering gram-negative microbial cell factories using transposon vectors. Methods Mol Biol 2017; 1498:273–293
     [Google Scholar]
  122. Martínez-García E, de Lorenzo V. Molecular tools and emerging strategies for deep genetic/genomic refactoring of Pseudomonas . Curr Opin Biotechnol 2017; 47:120–132 [View Article]
     [Google Scholar]
  123. Lieder S, Nikel PI, de Lorenzo V, Takors R. Genome reduction boosts heterologous gene expression in Pseudomonas putida. Microb Cell Fact 2015; 14:23 [View Article]
     [Google Scholar]
  124. Sánchez-Pascuala A, Fernández-Cabezón L, de Lorenzo V, Nikel PI. Functional implementation of a linear glycolysis for sugar catabolism in Pseudomonas putida . Metab Eng 2019; 54:200–211 [View Article]
     [Google Scholar]
  125. Poblete-Castro I, Becker J, Dohnt K, dos Santos VM, Wittmann C. Industrial biotechnology of Pseudomonas putida and related species. Appl Microbiol Biotechnol 2012; 93:2279–2290 [View Article]
     [Google Scholar]
  126. Prieto A, Escapa IF, Martínez V, Dinjaski N, Herencias C et al. A holistic view of polyhydroxyalkanoate metabolism in Pseudomonas putida . Environ Microbiol 2016; 18:341–357 [View Article]
     [Google Scholar]
  127. Wittgens A, Tiso T, Arndt TT, Wenk P, Hemmerich J et al. Growth independent rhamnolipid production from glucose using the non-pathogenic Pseudomonas putida KT2440. Microb Cell Fact 2011; 10:80 [View Article]
     [Google Scholar]
  128. Tiso T, Sabelhaus P, Behrens B, Wittgens A, Rosenau F et al. Creating metabolic demand as an engineering strategy in Pseudomonas putida - Rhamnolipid synthesis as an example. Metab Eng Commun 2016; 3:234–244 [View Article]
     [Google Scholar]
  129. Hernandez-Arranz S, Perez-Gil J, Marshall-Sabey D, Rodriguez-Concepcion M. Engineering Pseudomonas putida for isoprenoid production by manipulating endogenous and shunt pathways supplying precursors. Microb Cell Fact 2019; 18:152 [View Article]
     [Google Scholar]
  130. Lee S, Kang M, Bae J-H, Sohn J-H, Sung BH. Bacterial Valorization of lignin: strains, enzymes, conversion pathways, biosensors, and perspectives. Front Bioeng Biotechnol 2019; 7:209 [View Article]
     [Google Scholar]
  131. Xu Z, Lei P, Zhai R, Wen Z, Jin M. Recent advances in lignin valorization with bacterial cultures: microorganisms, metabolic pathways, and bio-products. Biotechnol Biofuels 2019; 12:32 [View Article]
     [Google Scholar]
  132. Kohlstedt M, Starck S, Barton N, Stolzenberger J, Selzer M et al. From lignin to nylon: Cascaded chemical and biochemical conversion using metabolically engineered Pseudomonas putida . Metab Eng 2018; 47:279–293 [View Article]
     [Google Scholar]
  133. Sniegowski PD, Gerrish PJ, Lenski RE. Evolution of high mutation rates in experimental populations of E. coli . Nature 1997; 387:703–705 [View Article]
     [Google Scholar]
  134. Baath E. Growth rates of bacterial communities in soils at varying pH: a comparison of the thymidine and leucine incorporation techniques. Microb Ecol 1998; 36:316–327
     [Google Scholar]
  135. Poulsen LK, Licht TR, Rang C, Krogfelt KA, Molin S. Physiological state of Escherichia coli BJ4 growing in the large intestines of streptomycin-treated mice. J Bacteriol 1995; 177:5840–5845 [View Article]
     [Google Scholar]
  136. Foster PL. Mechanisms of stationary phase mutation: a decade of adaptive mutation. Annu Rev Genet 1999; 33:57–88 [View Article]
     [Google Scholar]
  137. Rosenberg SM. Evolving responsively: adaptive mutation. Nat Rev Genet 2001; 2:504–515 [View Article]
     [Google Scholar]
  138. Metzgar D, Wills C. Evidence for the adaptive evolution of mutation rates. Cell 2000; 101:581–584 [View Article]
     [Google Scholar]
  139. Tenaillon O, Taddei F, Radman M, Matic I. Second-Order selection in bacterial evolution: selection acting on mutation and recombination rates in the course of adaptation. Res Microbiol 2001; 152:11–16 [View Article]
     [Google Scholar]
  140. Foster PL. Stress-Induced mutagenesis in bacteria. Crit Rev Biochem Mol Biol 2007; 42:373–397 [View Article]
     [Google Scholar]
  141. Bjedov I et al. Stress-Induced mutagenesis in bacteria. Science 2003; 300:1404–1409 [View Article]
     [Google Scholar]
  142. Miller JH. Perspective on mutagenesis and repair: the standard model and alternate modes of mutagenesis. Crit Rev Biochem Mol Biol 2005; 40:155–179 [View Article]
     [Google Scholar]
  143. Kivisaar M. Stationary phase mutagenesis: mechanisms that accelerate adaptation of microbial populations under environmental stress. Environ Microbiol 2003; 5:814–827 [View Article]
     [Google Scholar]
  144. Robleto EA, Yasbin R, Ross C, Pedraza-Reyes M. Stationary phase mutagenesis in B. subtilis: a paradigm to study genetic diversity programs in cells under stress. Crit Rev Biochem Mol Biol 2007; 42:327–339 [View Article]
     [Google Scholar]
  145. Galhardo RS, Hastings PJ, Rosenberg SM. Mutation as a stress response and the regulation of evolvability. Crit Rev Biochem Mol Biol 2007; 42:399–435 [View Article]
     [Google Scholar]
  146. Ponder RG, Fonville NC, Rosenberg SM. A switch from high-fidelity to error-prone DNA double-strand break repair underlies stress-induced mutation. Mol Cell 2005; 19:791–804 [View Article]
     [Google Scholar]
  147. Shee C, Gibson JL, Darrow MC, Gonzalez C, Rosenberg SM. Impact of a stress-inducible switch to mutagenic repair of DNA breaks on mutation in Escherichia coli . Proc Natl Acad Sci U S A 2011; 108:13659–13664 [View Article]
     [Google Scholar]
  148. Rosenberg SM, Shee C, Frisch RL, Hastings PJ. Stress-induced mutation via DNA breaks in Escherichia coli: a molecular mechanism with implications for evolution and medicine. BioEssays 2012; 34:885–892 [View Article]
     [Google Scholar]
  149. Williams AB, Foster PL. Stress-Induced mutagenesis. EcoSal Plus 2012; 5: [View Article]
     [Google Scholar]
  150. Cairns J, Foster PL. Adaptive reversion of a frameshift mutation in Escherichia coli . Genetics 1991; 128:695–701
     [Google Scholar]
  151. Kasak L, Hõrak R, Kivisaar M. Promoter-creating mutations in Pseudomonas putida: a model system for the study of mutation in starving bacteria. Proc Natl Acad Sci U S A 1997; 94:3134–3139 [View Article]
     [Google Scholar]
  152. Tsuda M, Iino T. Genetic analysis of a transposon carrying toluene degrading genes on a TOL plasmid pWWO. Mol Gen Genet 1987; 210:270–276 [View Article]
     [Google Scholar]
  153. Reddy BR, Shaw LE, Sayers JR, Williams PA. Two identical copies of IS1246, a 1275 base pair sequence related to other bacterial insertion sequences, enclose the xyl genes on TOL plasmid pWWO. Microbiology 1994; 140:2305–2307 [View Article]
     [Google Scholar]
  154. Meulien P, Broda P. Identification of chromosomally integrated TOL DNA in cured derivatives of Pseudomonas putida PaW1. J Bacteriol 1982; 152:911–914
     [Google Scholar]
  155. Nurk A, Tamm A, Hôrak R, Kivisaar M. In-vivo-generated fusion promoters in Pseudomonas putida . Gene 1993; 127:23–29 [View Article]
     [Google Scholar]
  156. Ilves H, Hõrak R, Kivisaar M. Involvement of S in starvation-induced transposition of Pseudomonas putida transposon Tn4652. J Bacteriol 2001; 183:5445–5448 [View Article]
     [Google Scholar]
  157. Ilves H, Hõrak R, Teras R, Kivisaar M. IHF is the limiting host factor in transposition of Pseudomonas putida transposon Tn4652 in stationary phase. Mol Microbiol 2004; 51:1773–1785 [View Article]
     [Google Scholar]
  158. Foster P, Trimarchi J. Adaptive reversion of a frameshift mutation in Escherichia coli by simple base deletions in homopolymeric runs. Science 1994; 265:407–409 [View Article]
     [Google Scholar]
  159. Rosenberg S, Longerich S, Gee P, Harris R. Adaptive mutation by deletions in small mononucleotide repeats. Science 1994; 265:405–407 [View Article]
     [Google Scholar]
  160. Saumaa S, Tover A, Kasak L, Kivisaar M. Different spectra of stationary-phase mutations in early-arising versus late-arising mutants of Pseudomonas putida: involvement of the DNA repair enzyme MutY and the stationary-phase sigma factor RpoS. J Bacteriol 2002; 184:6957–6965 [View Article]
     [Google Scholar]
  161. Tegova R, Tover A, Tarassova K, Tark M, Kivisaar M. Involvement of error-prone DNA polymerase IV in stationary-phase mutagenesis in Pseudomonas putida . J Bacteriol 2004; 186:2735–2744 [View Article]
     [Google Scholar]
  162. Reardon JT, Sancar A. Nucleotide excision repair. Prog Nucleic Acid Res Mol Biol 2005; 79:183–235 [View Article]
     [Google Scholar]
  163. Tark M, Tover A, Koorits L, Tegova R, Kivisaar M. Dual role of NER in mutagenesis in Pseudomonas putida . DNA Repair 2008; 7:20–30 [View Article]
     [Google Scholar]
  164. Koorits L, Tegova R, Tark M, Tarassova K, Tover A et al. Study of involvement of ImuB and DnaE2 in stationary-phase mutagenesis in Pseudomonas putida . DNA Repair 2007; 6:863–868 [View Article]
     [Google Scholar]
  165. Jatsenko T, Sidorenko J, Saumaa S, Kivisaar M. DNA Polymerases ImuC and DinB Are Involved in DNA Alkylation Damage Tolerance in Pseudomonas aeruginosa and Pseudomonas putida . PLoS One 2017; 12:e0170719 [View Article]
     [Google Scholar]
  166. Erill I, Campoy S, Mazon G, Barbe J. Dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain. Nucleic Acids Res 2006; 34:66–77 [View Article]
     [Google Scholar]
  167. Kivisaar M. Mechanisms of stationary-phase mutagenesis in bacteria: mutational processes in pseudomonads. FEMS Microbiol Lett 2010; 312:1–14 [View Article]
     [Google Scholar]
  168. Permina EA, Mironov AA, Gelfand MS. Damage-repair error-prone polymerases of eubacteria: association with mobile genome elements. Gene 2002; 293:133–140 [View Article]
     [Google Scholar]
  169. Tark M, Tover A, Tarassova K, Tegova R, Kivi G et al. A DNA polymerase V homologue encoded by TOL plasmid pWW0 confers evolutionary fitness on Pseudomonas putida under conditions of environmental stress. J Bacteriol 2005; 187:5203–5213 [View Article]
     [Google Scholar]
  170. KS J, Parales RE. Nitroaromatic compounds, from synthesis to biodegradation. Microbiol Mol Biol Rev: MMBR 2010; 74:250–272
     [Google Scholar]
  171. Kivisaar M. Degradation of nitroaromatic compounds: a model to study evolution of metabolic pathways. Mol Microbiol 2009; 74:777–781 [View Article]
     [Google Scholar]
  172. van der Meer JR, Sentchilo V. Genomic islands and the evolution of catabolic pathways in bacteria. Curr Opin Biotechnol 2003; 14:248–254 [View Article]
     [Google Scholar]
  173. Juhas M, van der Meer JR, Gaillard M, Harding RM, Hood DW et al. Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev 2009; 33:376–393 [View Article]
     [Google Scholar]
  174. Nojiri H, Shintani M, Omori T. Divergence of mobile genetic elements involved in the distribution of xenobiotic-catabolic capacity. Appl Microbiol Biotechnol 2004; 64:154–174 [View Article]
     [Google Scholar]
  175. Norman A, Hansen LH, Sørensen SJ. Conjugative plasmids: vessels of the communal gene pool. Philosophical Transactions of the Royal Society B: Biological Sciences 2009; 364:2275–2289 [View Article]
     [Google Scholar]
  176. Tavita K, Mikkel K, Tark-Dame M, Jerabek H, Teras R et al. Homologous recombination is facilitated in starving populations of Pseudomonas putida by phenol stress and affected by chromosomal location of the recombination target. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 2012; 737:12–24 [View Article]
     [Google Scholar]
  177. Martínez-García E, Jatsenko T, Kivisaar M, de Lorenzo V. Freeing P seudomonas putida KT2440 of its proviral load strengthens endurance to environmental stresses. Environ Microbiol 2015; 17:76–90 [View Article]
     [Google Scholar]
  178. Juurik T, Ilves H, Teras R, Ilmjärv T, Tavita K et al. Mutation frequency and spectrum of mutations vary at different chromosomal positions of Pseudomonas putida . PLoS One 2012; 7:e48511 [View Article]
     [Google Scholar]
  179. Ukkivi K, Kivisaar M. Involvement of transcription-coupled repair factor Mfd and DNA helicase UvrD in mutational processes in Pseudomonas putida . DNA Repair 2018; 72:18–27 [View Article]
     [Google Scholar]
  180. Tagel M, Tavita K, Hõrak R, Kivisaar M, Ilves H. A novel papillation assay for the identification of genes affecting mutation rate in Pseudomonas putida and other pseudomonads. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 2016; 790:41–55 [View Article]
     [Google Scholar]
  181. Akkaya Özlem, Pérez-Pantoja DR, Calles B, Nikel PI, de Lorenzo V et al. The Metabolic Redox Regime of Pseudomonas putida Tunes Its Evolvability toward Novel Xenobiotic Substrates. MBio 2018; 9:
     [Google Scholar]
  182. Ilmjärv T, Naanuri E, Kivisaar M. Contribution of increased mutagenesis to the evolution of pollutants-degrading Indigenous bacteria. PLoS One 2017; 12:e0182484 [View Article]
     [Google Scholar]
  183. Berendsen RL, Pieterse CMJ, Bakker PAHM. The rhizosphere microbiome and plant health. Trends Plant Sci 2012; 17:478–486 [View Article]
     [Google Scholar]
  184. Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S et al. The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev 2015; 79:293–320 [View Article]
     [Google Scholar]
  185. Haas D, Défago G. Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat Rev Microbiol 2005; 3:307–319 [View Article]
     [Google Scholar]
  186. Lugtenberg BJ, Dekkers L, Bloemberg GV. Molecular determinants of rhizosphere colonization by Pseudomonas . Annu Rev Phytopathol 2001; 39:461–490 [View Article]
     [Google Scholar]
  187. Pizarro-Tobías P, Fernández M, Niqui JL, Solano J, Duque E et al. Restoration of a Mediterranean forest after a fire: bioremediation and rhizoremediation field-scale trial. Microb Biotechnol 2015; 8:77–92 [View Article]
     [Google Scholar]
  188. Weyens N, Truyens S, Dupae J, Newman L, Taghavi S et al. Potential of the TCE-degrading endophyte Pseudomonas putida W619-TCE to improve plant growth and reduce TCE phytotoxicity and evapotranspiration in poplar cuttings. Environ Pollut 2010; 158:2915–2919 [View Article]
     [Google Scholar]
  189. Li J, McConkey BJ, Cheng Z, Guo S, Glick BR. Identification of plant growth-promoting bacteria-responsive proteins in cucumber roots under hypoxic stress using a proteomic approach. J Proteomics 2013; 84:119–131 [View Article]
     [Google Scholar]
  190. Maroniche GA, Rubio EJ, Consiglio A, Perticari A. Plant-associated fluorescent Pseudomonas from red lateritic soil: Beneficial characteristics and their impact on lettuce growth. J Gen Appl Microbiol 2016; 62:248–257 [View Article]
     [Google Scholar]
  191. Molina L et al. Survival of Pseudomonas putida KT2440 in soil and in the rhizosphere of plants under greenhouse and environmental conditions. Soil Biol Biochem 2000; 32:315–321 [View Article]
     [Google Scholar]
  192. Simons M, van der Bij AJ, Brand I, de Weger LA, Wijffelman CA et al. Gnotobiotic system for studying rhizosphere colonization by plant growth-promoting Pseudomonas bacteria. Mol Plant Microbe Interact 1996; 9:600–607 [View Article]
     [Google Scholar]
  193. Bogino P, Oliva M, Sorroche F, Giordano W. The role of bacterial biofilms and surface components in plant-bacterial associations. Int J Mol Sci 2013; 14:15838–15859 [View Article]
     [Google Scholar]
  194. Ghirardi S, Dessaint F, Mazurier S, Corberand T, Raaijmakers JM et al. Identification of traits shared by rhizosphere-competent strains of fluorescent pseudomonads. Microb Ecol 2012; 64:725–737 [View Article]
     [Google Scholar]
  195. Pandin C, Le Coq D, Canette A, Aymerich S, Briandet R. Should the biofilm mode of life be taken into consideration for microbial biocontrol agents?. Microb Biotechnol 2017; 10:719–734 [View Article]
     [Google Scholar]
  196. Martínez-Gil M, Quesada JM, Ramos-González MI, Soriano MI, de Cristóbal RE et al. Interplay between extracellular matrix components of Pseudomonas putida biofilms. Res Microbiol 2013; 164:382–389 [View Article]
     [Google Scholar]
  197. Duque E, de la Torre J, Bernal P, Molina-Henares MA, Alaminos M et al. Identification of reciprocal adhesion genes in pathogenic and non-pathogenic Pseudomonas . Environ Microbiol 2013; 15:36–48 [View Article]
     [Google Scholar]
  198. Martínez-Gil M, Yousef-Coronado F, Espinosa-Urgel M, LapF E-UM. Lapf, the second largest Pseudomonas putida protein, contributes to plant root colonization and determines biofilm architecture. Mol Microbiol 2010; 77:549–561 [View Article]
     [Google Scholar]
  199. Yousef-Coronado Fátima, Travieso María L., Espinosa-Urgel M, Travieso ML, Different E-UM. Different, overlapping mechanisms for colonization of abiotic and plant surfaces by Pseudomonas putida . FEMS Microbiol Lett 2008; 288:118–124
     [Google Scholar]
  200. Espinosa-Urgel M, Salido A, Ramos J-L. Genetic analysis of functions involved in adhesion of Pseudomonas putida to seeds. J Bacteriol 2000; 182:2363–2369 [View Article]
     [Google Scholar]
  201. González-Gil G, Bringmann P, Kahmann R. FIS is a regulator of metabolism in Escherichia coli . Mol Microbiol 1996; 22:21–29 [View Article]
     [Google Scholar]
  202. Moor H, Teppo A, Lahesaare A, Kivisaar M, Teras R. Fis overexpression enhances Pseudomonas putida biofilm formation by regulating the ratio of LapA and LapF. Microbiology 2014; 160:2681–2693 [View Article]
     [Google Scholar]
  203. Jakovleva J, Teppo A, Velts A, Saumaa S, Moor H et al. Fis regulates the competitiveness of Pseudomonas putida on barley roots by inducing biofilm formation. Microbiology 2012; 158:708–720 [View Article]
     [Google Scholar]
  204. Matilla MA, Espinosa-Urgel M, Rodríguez-Herva JJ, Ramos JL, Ramos-González M. Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere. Genome Biol 2007; 8:R179 [View Article]
     [Google Scholar]
  205. Efremov RG, Baradaran R, Sazanov LA. The architecture of respiratory complex I. Nature 2010; 465:441–445 [View Article]
     [Google Scholar]
  206. Esterházy D, King MS, Yakovlev G, Hirst J. Production of reactive oxygen species by complex I (NADH:Ubiquinone Oxidoreductase) from Escherichia coli and comparison to the enzyme from mitochondria. Biochemistry 2008; 47:3964–3971 [View Article]
     [Google Scholar]
  207. Camacho Carvajal MM, Wijfjes AHM, Mulders IHM, Lugtenberg BJJ, Bloemberg GV. Characterization of NADH Dehydrogenases of Pseudomonas fluorescens WCS365 and their role in competitive root colonization. MPMI 2002; 15:662–671 [View Article]
     [Google Scholar]
  208. Teppo A, Lahesaare A, Ainelo H, Samuel K, Kivisaar M et al. Colonization efficiency of Pseudomonas putida is influenced by Fis-controlled transcription of nuoA-N operon. PLoS One 2018; 13:e0201841 [View Article]
     [Google Scholar]
  209. Udaondo Z, Molina L, Segura A, Duque E, Ramos JL. Analysis of the core genome and pangenome of P seudomonas putida . Environ Microbiol 2016; 18:3268–3283 [View Article]
     [Google Scholar]
  210. Taghavi S, Garafola C, Monchy S, Newman L, Hoffman A et al. Genome survey and characterization of endophytic bacteria exhibiting a beneficial effect on growth and development of poplar trees. Appl Environ Microbiol 2009; 75:748–757 [View Article]
     [Google Scholar]
  211. Meziane H, VAN DER Sluis I, VAN Loon LC, Höfte M, Bakker PAHM. Determinants of Pseudomonas putida WCS358 involved in inducing systemic resistance in plants. Mol Plant Pathol 2005; 6:177–185 [View Article]
     [Google Scholar]
  212. Matilla MA, Ramos JL, Bakker PAHM, Doornbos R, Badri DV et al. Pseudomonas putida KT2440 causes induced systemic resistance and changes in Arabidopsis root exudation. Environ Microbiol Rep 2010; 2:381–388 [View Article]
     [Google Scholar]
  213. Bernal P, Allsopp LP, Filloux A, Llamas MA. The Pseudomonas putida T6SS is a plant warden against phytopathogens. ISME J 2017; 11:972–987 [View Article]
     [Google Scholar]
  214. BT H, Dong TG, Mekalanos JJ. A view to a kill: the bacterial type VI secretion system. Cell host & microbe 2014; 15:9–21
     [Google Scholar]
  215. Segura A, Ramos JL. Plant–bacteria interactions in the removal of pollutants. Curr Opin Biotechnol 2013; 24:467–473 [View Article]
     [Google Scholar]
  216. Kuiper I, Lagendijk EL, Bloemberg GV, Lugtenberg BJJ. Rhizoremediation: a beneficial plant-microbe interaction. Mol Plant Microbe Interact 2004; 17:6–15 [View Article]
     [Google Scholar]
  217. Fernández M, Niqui-Arroyo JL, Conde S, Ramos JL, Duque E. Enhanced tolerance to naphthalene and enhanced rhizoremediation performance for Pseudomonas putida KT2440 via the NAH7 catabolic plasmid. Appl Environ Microbiol 2012; 78:5104–5110 [View Article]
     [Google Scholar]
  218. Von Graevenitz A, Weinstein J. Pathogenic significance of Pseudomonas fluorescens and Pseudomonas putida . Yale J Biol Med 1971; 44:265–273
     [Google Scholar]
  219. Aumeran C, Paillard C, Robin F, Kanold J, Baud O et al. Pseudomonas aeruginosa and Pseudomonas putida outbreak associated with contaminated water outlets in an oncohaematology paediatric unit. J Hosp Infect 2007; 65:47–53 [View Article]
     [Google Scholar]
  220. Bouallègue O, Mzoughi R, Weill F-X, Mahdhaoui N, Ben Salem Y et al. Outbreak of Pseudomonas putida bacteraemia in a neonatal intensive care unit. J Hosp Infect 2004; 57:88–91 [View Article]
     [Google Scholar]
  221. Ladhani S, Bhutta ZA. Neonatal Pseudomonas putida infection presenting as staphylococcal scalded skin syndrome. Eur J Clin Microbiol Infect Dis 1998; 17:642–644 [View Article]
     [Google Scholar]
  222. Taylor M, Keane C, Falkiner F. Pseudomonas putida in transfused blood. The Lancet 1984; 324:107 [View Article]
     [Google Scholar]
  223. Yoshino Y, Kitazawa T, Kamimura M, Tatsuno K, Ota Y, Yotsuyanagi H et al. Pseudomonas putida bacteremia in adult patients: five case reports and a review of the literature. J Infect Chemother 2011; 17:278–282 [View Article]
     [Google Scholar]
  224. Lombardi G, Luzzaro F, Docquier J-D, Riccio ML, Perilli M et al. Nosocomial infections caused by multidrug-resistant isolates of Pseudomonas putida producing VIM-1 metallo-beta-lactamase. J Clin Microbiol 2002; 40:4051–4055 [View Article]
     [Google Scholar]
  225. Erol S, Zenciroğlu A, Dilli D, Okumuş N, Aydin M et al. Evaluation of nosocomial blood stream infections caused by Pseudomonas species in newborns. Clin Lab 2014; 60:615–620 [View Article]
     [Google Scholar]
  226. Kim SE, Park S-H, Park HB, Park K-H, Kim S-H et al. Nosocomial Pseudomonas putida bacteremia: high rates of carbapenem resistance and mortality. Chonnam Med J 2012; 48:91–95 [View Article]
     [Google Scholar]
  227. Carpenter RJ, Hartzell JD, Forsberg JA, Babel BS, Ganesan A. Pseudomonas putida war wound infection in a US marine: a case report and review of the literature. J Infect 2008; 56:234–240 [View Article]
     [Google Scholar]
  228. Liu H, Zhao J, Xing Y, Li M, Du M et al. Nosocomial infection in adult admissions with hematological malignancies originating from different lineages: a prospective observational study. PLoS One 2014; 9:e113506 [View Article]
     [Google Scholar]
  229. Trevino M, Moldes L, Hernandez M, Martinez-Lamas L, Garcia-Riestra C et al. Nosocomial infection by VIM-2 metallo- -lactamase-producing Pseudomonas putida . J Med Microbiol 2010; 59:853–855 [View Article]
     [Google Scholar]
  230. Fernández M, Porcel M, de la Torre J, Molina-Henares MA, Daddaoua A et al. Analysis of the pathogenic potential of nosocomial Pseudomonas putida strains. Front Microbiol 2015; 6:871 [View Article]
     [Google Scholar]
  231. Molina L, Udaondo Z, Duque E, Fernández M, Molina-Santiago C et al. Antibiotic resistance determinants in a Pseudomonas putida strain isolated from a hospital. PLoS One 2014; 9:e81604 [View Article]
     [Google Scholar]
  232. Molina L, Udaondo Z, Duque E, Fernández M, Bernal P et al. Specific Gene Loci of Clinical Pseudomonas putida Isolates. PLoS One 2016; 11:e0147478 [View Article]
     [Google Scholar]
  233. Basso P, Wallet P, Elsen S, Soleilhac E, Henry T et al. Multiple Pseudomonas species secrete exolysin-like toxins and provoke Caspase-1-dependent macrophage death. Environ Microbiol 2017; 19:4045–4064 [View Article]
     [Google Scholar]
  234. Molina MA, Ramos J-L, Espinosa-Urgel M. A two-partner secretion system is involved in seed and root colonization and iron uptake by Pseudomonas putida KT2440. Environ Microbiol 2006; 8:639–647 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jmm/10.1099/jmm.0.001137
Loading

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error