User menu

Identification of novel toluene monooxygenase genes in a hydrocarbon-polluted sediment using sequence-and function-based screening of metagenomic libraries

Bibliographic reference Bouhajja, Emna ; McGuire , Micah ; Liles , Mark R. ; Bataille, Gwennaël ; Agathos, Spiros N. ; et. al. Identification of novel toluene monooxygenase genes in a hydrocarbon-polluted sediment using sequence-and function-based screening of metagenomic libraries. In: Applied Microbiology and Biotechnology, , p. 1-12 (2016)
Permanent URL
  1. Acheson Justin F., Bailey Lucas J., Elsen Nathaniel L., Fox Brian G., Structural basis for biomolecular recognition in overlapping binding sites in a diiron enzyme system, 10.1038/ncomms6009
  2. Allen J. P., Atekwana E. A., Atekwana E. A., Duris J. W., Werkema D. D., Rossbach S., The Microbial Community Structure in Petroleum-Contaminated Sediments Corresponds to Geophysical Signatures, 10.1128/aem.01752-06
  3. Anderson Iain, Held Brittany, Lapidus Alla, Nolan Matt, Lucas Susan, Tice Hope, Del Rio Tijana Glavina, Cheng Jan-Fang, Han Cliff, Tapia Roxanne, Goodwin Lynne A., Pitluck Sam, Liolios Konstantinos, Mavromatis Konstantinos, Pagani Ioanna, Ivanova Natalia, Mikhailova Natalia, Pati Amrita, Chen Amy, Palaniappan Krishna, Land Miriam, Brambilla Evelyne-Marie, Rohde Manfred, Spring Stefan, Göker Markus, Detter John C., Woyke Tanja, Bristow James, Eisen Jonathan A., Markowitz Victor, Hugenholtz Philip, Klenk Hans-Peter, Kyrpides Nikos C., Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4T), 10.4056/sigs.2746047
  4. Angov Evelina, Codon usage: Nature's roadmap to expression and folding of proteins, 10.1002/biot.201000332
  5. Anneser Bettina, Pilloni Giovanni, Bayer Anne, Lueders Tillmann, Griebler Christian, Einsiedl Florian, Richters Lars, High Resolution Analysis of Contaminated Aquifer Sediments and Groundwater—What Can be Learned in Terms of Natural Attenuation?, 10.1080/01490450903456723
  6. Bosch Rafael, Garcı́a-Valdés Elena, Moore Edward R.B., Genetic characterization and evolutionary implications of a chromosomally encoded naphthalene-degradation upper pathway from Pseudomonas stutzeri AN10, 10.1016/s0378-1119(99)00241-3
  7. Bouhajja Emna, Efthymiopoulos Theocharis, George Isabelle F., Moreels David, Van Houdt Rob, Mergeay Max, Agathos Spiros N., Conjugative transfer of broad host range plasmids to an acidobacterial strain, Edaphobacter aggregans, 10.1016/j.jbiotec.2016.01.025
  8. Brennerova Maria V., Josefiova Jirina, Brenner Vladimir, Pieper Dietmar H., Junca Howard, Metagenomics reveals diversity and abundance ofmeta-cleavage pathways in microbial communities from soil highly contaminated with jet fuel under air-sparging bioremediation, 10.1111/j.1462-2920.2009.01943.x
  9. Carmona M., Zamarro M. T., Blazquez B., Durante-Rodriguez G., Juarez J. F., Valderrama J. A., Barragan M. J. L., Garcia J. L., Diaz E., Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View, 10.1128/mmbr.00021-08
  10. Craig J. W., Chang F.-Y., Kim J. H., Obiajulu S. C., Brady S. F., Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad-Host-Range Cosmid Environmental DNA Libraries in Diverse Proteobacteria, 10.1128/aem.02169-09
  11. Dealtry Simone, Ding Guo-Chun, Weichelt Viola, Dunon Vincent, Schlüter Andreas, Martini María Carla, Papa María Florencia Del, Lagares Antonio, Amos Gregory Charles Auton, Wellington Elizabeth Margaret Helen, Gaze William Hugo, Sipkema Detmer, Sjöling Sara, Springael Dirk, Heuer Holger, van Elsas Jan Dirk, Thomas Christopher, Smalla Kornelia, Cultivation-Independent Screening Revealed Hot Spots of IncP-1, IncP-7 and IncP-9 Plasmid Occurrence in Different Environmental Habitats, 10.1371/journal.pone.0089922
  12. Dunon Vincent, Sniegowski Kristel, Bers Karolien, Lavigne Rob, Smalla Kornelia, Springael Dirk, High prevalence of IncP-1 plasmids and IS1071insertion sequences in on-farm biopurification systems and other pesticide-polluted environments, 10.1111/1574-6941.12173
  13. Ekkers David Matthias, Cretoiu Mariana Silvia, Kielak Anna Maria, van Elsas Jan Dirk, The great screen anomaly—a new frontier in product discovery through functional metagenomics, 10.1007/s00253-011-3804-3
  14. Entsch B, van Berkel WJ (1995) Structure and mechanism of para-hydroxybenzoate hydroxylase. FASEB J 9(7):476–483
  15. Ermolaeva MD (2001) Synonymous codon usage in bacteria. Curr Issues Mol Biol 3(4):91–97
  16. Fuchs Georg, Boll Matthias, Heider Johann, Microbial degradation of aromatic compounds — from one strategy to four, 10.1038/nrmicro2652
  17. Gao Junfeng, Ellis Lynda B. M., Wackett Lawrence P., The University of Minnesota Biocatalysis/Biodegradation Database: improving public access, 10.1093/nar/gkp771
  18. Garcia Costas Amaya M., Liu Zhenfeng, Tomsho Lynn P., Schuster Stephan C., Ward David M., Bryant Donald A., Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the phylum Acidobacteria : Candidatus Chloracidobacterium thermophilum genome, 10.1111/j.1462-2920.2011.02592.x
  19. George Isabelle F., Liles Mark R., Hartmann Manuela, Ludwig Wolfgang, Goodman Robert M., Agathos Spiros N., Changes in soilAcidobacteriacommunities after 2,4,6-trinitrotoluene contamination, 10.1111/j.1574-6968.2009.01632.x
  20. Gillespie D. E., Brady S. F., Bettermann A. D., Cianciotto N. P., Liles M. R., Rondon M. R., Clardy J., Goodman R. M., Handelsman J., Isolation of Antibiotics Turbomycin A and B from a Metagenomic Library of Soil Microbial DNA, 10.1128/aem.68.9.4301-4306.2002
  21. Gross Sherilyn A., Avens Heather J., Banducci Amber M., Sahmel Jennifer, Panko Julie M., Tvermoes Brooke E., Analysis of BTEX groundwater concentrations from surface spills associated with hydraulic fracturing operations, 10.1080/10962247.2012.759166
  22. Heider Johann, Spormann Alfred M., Beller Harry R., Widdel Friedrich, Anaerobic bacterial metabolism of hydrocarbons, 10.1111/j.1574-6976.1998.tb00381.x
  23. Hendrickx B., Dejonghe W., Boenne W., Brennerova M., Cernik M., Lederer T., Bucheli-Witschel M., Bastiaens L., Verstraete W., Top E. M., Diels L., Springael D., Dynamics of an Oligotrophic Bacterial Aquifer Community during Contact with a Groundwater Plume Contaminated with Benzene, Toluene, Ethylbenzene, and Xylenes: an In Situ Mesocosm Study, 10.1128/aem.71.7.3815-3825.2005
  24. Hendrickx Barbara, Dejonghe Winnie, Faber Folkert, Boënne Wesley, Bastiaens Leen, Verstraete Willy, Top Eva M., Springael Dirk, PCR-DGGE method to assess the diversity of BTEX mono-oxygenase genes at contaminated sites : BTEX mono-oxygenase genes assessed by PCR-DGGE, 10.1111/j.1574-6941.2005.00018.x
  25. Jackson C, Harper J, Willoughby D, Roden E, Churchill P (1997) A simple, efficient method for the separation of humic substances and DNA from environmental samples. Appl Environ Microbiol 63(12):4993–4995
  26. Jacquiod Samuel, Demanèche Sandrine, Franqueville Laure, Ausec Luka, Xu Zhuofei, Delmont Tom O., Dunon Vincent, Cagnon Christine, Mandic-Mulec Ines, Vogel Timothy M., Simonet Pascal, Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library, 10.1016/j.jbiotec.2014.03.036
  27. Janssen Paul J., Van Houdt Rob, Moors Hugo, Monsieurs Pieter, Morin Nicolas, Michaux Arlette, Benotmane Mohammed A., Leys Natalie, Vallaeys Tatiana, Lapidus Alla, Monchy Sébastien, Médigue Claudine, Taghavi Safiyh, McCorkle Sean, Dunn John, van der Lelie Daniël, Mergeay Max, The Complete Genome Sequence of Cupriavidus metallidurans Strain CH34, a Master Survivalist in Harsh and Anthropogenic Environments, 10.1371/journal.pone.0010433
  28. Jobelius Carsten, Ruth Bettina, Griebler Christian, Meckenstock Rainer U., Hollender Juliane, Reineke Anne, Frimmel Fritz H., Zwiener Christian, Metabolites Indicate Hot Spots of Biodegradation and Biogeochemical Gradients in a High-Resolution Monitoring Well, 10.1021/es1030867
  29. Johnson GR, Olsen RH (1997) Multiple pathways for toluene degradation in Burkholderia sp. strain JS150. Appl Environ Microbiol 63(10):4047–4052
  30. Kahng Hyung-Yeel, Cho Kun, Song Seung-Yual, Kim Soo-Jung, Leem Sun-Hee, Kim Seung Il, Enhanced detection and characterization of protocatechuate 3,4-dioxygenase in Acinetobacter lwoffii K24 by proteomics using a column separation, 10.1016/s0006-291x(02)00778-7
  31. Kakirde Kavita S., Wild Jadwiga, Godiska Ronald, Mead David A., Wiggins Andrew G., Goodman Robert M., Szybalski Waclaw, Liles Mark R., Gram negative shuttle BAC vector for heterologous expression of metagenomic libraries, 10.1016/j.gene.2010.11.004
  32. Kielak A. M., van Veen J. A., Kowalchuk G. A., Comparative Analysis of Acidobacterial Genomic Fragments from Terrestrial and Aquatic Metagenomic Libraries, with Emphasis on Acidobacteria Subdivision 6, 10.1128/aem.00343-10
  33. Kimura Nobutada, Sakai Kayoko, Nakamura Kazunori, Isolation and Characterization of a 4-Nitrotoluene-Oxidizing Enzyme from Activated Sludge by a Metagenomic Approach, 10.1264/jsme2.me10110
  34. Larentis Michael, Hoermann Katrin, Lueders Tillmann, Fine-scale degrader community profiling over an aerobic/anaerobic redox gradient in a toluene-contaminated aquifer : Degrader distribution at a hydrocarbon plume, 10.1111/1758-2229.12004
  35. Lau Peter C.K., Bergeron Héléne, Labbé Diane, Wang Ying, Brousseau Roland, Gibson David T., Sequence and expression of the todGIH genes involved in the last three steps of toluene degradation by Pseudomonas putida F1, 10.1016/0378-1119(94)90827-3
  36. Lee Eun-Hee, Ryu Hee Wook, Cho Kyung-Suk, Effect of switching gas inlet position on the performance of a polyurethane biofilter under transient loading for the removal of benzene, toluene and xylene mixtures, 10.1080/10934529.2011.609444
  37. Lee Sang-Hwan, Lee Won-Seok, Lee Chang-Ho, Kim Jeong-Gyu, Degradation of phenanthrene and pyrene in rhizosphere of grasses and legumes, 10.1016/j.jhazmat.2007.09.041
  38. Leis Benedikt, Angelov Angel, Liebl Wolfgang, Screening and Expression of Genes from Metagenomes, Advances in Applied Microbiology (2013) ISBN:9780124076785 p.1-68, 10.1016/b978-0-12-407678-5.00001-5
  39. Liles M. R., Williamson L. L., Rodbumrer J., Torsvik V., Goodman R. M., Handelsman J., Recovery, Purification, and Cloning of High-Molecular-Weight DNA from Soil Microorganisms, 10.1128/aem.02630-07
  40. Meckenstock Rainer U., Elsner Martin, Griebler Christian, Lueders Tillmann, Stumpp Christine, Aamand Jens, Agathos Spiros N., Albrechtsen Hans-Jørgen, Bastiaens Leen, Bjerg Poul L., Boon Nico, Dejonghe Winnie, Huang Wei E., Schmidt Susanne I., Smolders Erik, Sørensen Sebastian R., Springael Dirk, van Breukelen Boris M., Biodegradation: Updating the Concepts of Control for Microbial Cleanup in Contaminated Aquifers, 10.1021/acs.est.5b00715
  41. Mergeay M, Houba C, Gerits J (1978) Extrachromosomal inheritance controlling resistance to cadmium, cobalt, copper and zinc ions: evidence from curing in a Pseudomonas. Arch Int Physiol Biochim 86(2):440–442
  42. Mettel C., Kim Y., Shrestha P. M., Liesack W., Extraction of mRNA from Soil, 10.1128/aem.03047-09
  43. Notomista Eugenio, Lahm Armin, Di Donato Alberto, Tramontano Anna, Evolution of Bacterial and Archaeal Multicomponent Monooxygenases, 10.1007/s00239-002-2414-1
  44. Ochman Howard, Lawrence Jeffrey G., Groisman Eduardo A., 10.1038/35012500
  45. Okunishi Suguru, Morita Yasutaka, Higuchi Takashi, Maeda Hiroto, Nishi Katsuji, Transformation of microflora during degradation of gaseous toluene in a biofilter detected using PCR-DGGE, 10.1080/10962247.2012.672396
  46. Olsen R H, Kukor J J, Kaphammer B, A novel toluene-3-monooxygenase pathway cloned from Pseudomonas pickettii PKO1., 10.1128/jb.176.12.3749-3756.1994
  47. Pansegrau Werner, Lanka Erich, Barth Peter T., Figurski David H., Guiney Donald G., Haas Dieter, Helinski Donald R., Schwab Helmut, Stanisich Vilma A., Thomas Christopher M., Complete Nucleotide Sequence of Birmingham IncPα Plasmids, 10.1006/jmbi.1994.1404
  48. Parsley Larissa C., Linneman Jonathan, Goode Ann M., Becklund Kristen, George Isabelle, Goodman Robert M., Lopanik Nicole B., Liles Mark R., Polyketide synthase pathways identified from a metagenomic library are derived from soil Acidobacteria : Polyketide synthase pathways from soil Acidobacteria, 10.1111/j.1574-6941.2011.01122.x
  49. Patil Kaustubh Raosaheb, Roune Linus, McHardy Alice Carolyn, The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences, 10.1371/journal.pone.0038581
  50. Rakoczy Jana, Remy Benjamin, Vogt Carsten, Richnow Hans H., A Bench-Scale Constructed Wetland As a Model to Characterize Benzene Biodegradation Processes in Freshwater Wetlands, 10.1021/es2026196
  51. Rawat Suman R., Männistö Minna K., Starovoytov Valentin, Goodwin Lynne, Nolan Matt, Hauser Lauren, Land Miriam, Davenport Karen Walston, Woyke Tanja, Häggblom Max M., Complete genome sequence of Terriglobus saanensis type strain SP1PR4T, an Acidobacteria from tundra soil, 10.4056/sigs.3036810
  52. Rondon M. R., August P. R., Bettermann A. D., Brady S. F., Grossman T. H., Liles M. R., Loiacono K. A., Lynch B. A., MacNeil I. A., Minor C., Tiong C. L., Gilman M., Osburne M. S., Clardy J., Handelsman J., Goodman R. M., Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and Functional Diversity of Uncultured Microorganisms, 10.1128/aem.66.6.2541-2547.2000
  53. Saul David J., Aislabie Jackie M., Brown Caroline E., Harris Lisa, Foght Julia M., Hydrocarbon contamination changes the bacterial diversity of soil from around Scott Base, Antarctica, 10.1016/j.femsec.2004.11.007
  54. Scow Kate M, Hicks Kristin A, Natural attenuation and enhanced bioremediation of organic contaminants in groundwater, 10.1016/j.copbio.2005.03.009
  55. Sevastsyanovich Y. R., Krasowiak R., Bingle L. E. H., Haines A. S., Sokolov S. L., Kosheleva I. A., Leuchuk A. A., Titok M. A., Smalla K., Thomas C. M., Diversity of IncP-9 plasmids of Pseudomonas, 10.1099/mic.0.2008/017939-0
  56. Sharma Pushpender K., Capalash Neena, Kaur Jagdeep, An improved method for single step purification of metagenomic DNA, 10.1007/s12033-007-0015-3
  57. Sierra-García Isabel Natalia, Correa Alvarez Javier, Pantaroto de Vasconcellos Suzan, Pereira de Souza Anete, dos Santos Neto Eugenio Vaz, de Oliveira Valéria Maia, New Hydrocarbon Degradation Pathways in the Microbial Metagenome from Brazilian Petroleum Reservoirs, 10.1371/journal.pone.0090087
  58. Singleton D. R., Hu J., Aitken M. D., Heterologous Expression of Polycyclic Aromatic Hydrocarbon Ring-Hydroxylating Dioxygenase Genes from a Novel Pyrene-Degrading Betaproteobacterium, 10.1128/aem.00173-12
  59. Suenaga Hikaru, Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities : Targeted metagenomics, 10.1111/j.1462-2920.2011.02438.x
  60. Suenaga Hikaru, Ohnuki Tsutomu, Miyazaki Kentaro, Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compounds, 10.1111/j.1462-2920.2007.01342.x
  61. Szczepanowski Rafael, Eikmeyer Felix, Harfmann Jannis, Blom Jochen, Rogers Linda M., Top Eva M., Schlüter Andreas, Sequencing and comparative analysis of IncP-1α antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions, 10.1016/j.jbiotec.2010.11.018
  62. Taghavi S, van der Lelie D, Mergeay M (1994) Electroporation of Alcaligenes eutrophus with (mega) plasmids and genomic DNA fragments. Appl Environ Microbiol 60(10):3585–3591
  63. Trevors JT, Starodub ME (1990) Electroporation of pKK1 silver-resistance plasmid from Pseudomonas stutzeri AG259 into Pseudomonas putida CYM318, vol 21. Springer, New York
  64. van Elsas Jan Dirk, Costa Rodrigo, Jansson Janet, Sjöling Sara, Bailey Mark, Nalin Renaud, Vogel Timothy M., van Overbeek Leo, The metagenomics of disease-suppressive soils – experiences from the METACONTROL project, 10.1016/j.tibtech.2008.07.004
  65. Vishnivetskaya T. A., Mosher J. J., Palumbo A. V., Yang Z. K., Podar M., Brown S. D., Brooks S. C., Gu B., Southworth G. R., Drake M. M., Brandt C. C., Elias D. A., Mercury and Other Heavy Metals Influence Bacterial Community Structure in Contaminated Tennessee Streams, 10.1128/aem.01715-10
  66. Wang Ying, Rawlings Merriann, Gibson David T., Labb� Diane, Bergeron H�l�ne, Brousseau Roland, Lau Peter C. K., Identification of a membrane protein and a truncated LysR-type regulator associated with the toluene degradation pathway in Pseudomonas putida F1, 10.1007/bf00298963
  67. Ward N. L., Challacombe J. F., Janssen P. H., Henrissat B., Coutinho P. M., Wu M., Xie G., Haft D. H., Sait M., Badger J., Barabote R. D., Bradley B., Brettin T. S., Brinkac L. M., Bruce D., Creasy T., Daugherty S. C., Davidsen T. M., DeBoy R. T., Detter J. C., Dodson R. J., Durkin A. S., Ganapathy A., Gwinn-Giglio M., Han C. S., Khouri H., Kiss H., Kothari S. P., Madupu R., Nelson K. E., Nelson W. C., Paulsen I., Penn K., Ren Q., Rosovitz M. J., Selengut J. D., Shrivastava S., Sullivan S. A., Tapia R., Thompson L. S., Watkins K. L., Yang Q., Yu C., Zafar N., Zhou L., Kuske C. R., Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils, 10.1128/aem.02294-08
  68. Wexler Margaret, Johnston Andrew W. B., Wide Host-Range Cloning for Functional Metagenomics, Methods in Molecular Biology (2010) ISBN:9781607618225 p.77-96, 10.1007/978-1-60761-823-2_5
  69. Whited G M, Gibson D T, Separation and partial characterization of the enzymes of the toluene-4-monooxygenase catabolic pathway in Pseudomonas mendocina KR1., 10.1128/jb.173.9.3017-3020.1991
  70. Winderl C., Anneser B., Griebler C., Meckenstock R. U., Lueders T., Depth-Resolved Quantification of Anaerobic Toluene Degraders and Aquifer Microbial Community Patterns in Distinct Redox Zones of a Tar Oil Contaminant Plume, 10.1128/aem.01951-07
  71. Yoon Young-Ho, Yun Sung-Ho, Park Soon-Ho, Seol So-Young, Leem Sun-Hee, Kim Seung Il, Characterization of a new catechol branch of the β-ketoadipate pathway induced for benzoate degradation in Acinetobacter lwoffii K24, 10.1016/j.bbrc.2007.05.132
  72. Zhou JZ, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62(2):316–322